Shape (MGW) (no nucleotides) Example with fixed values for nucleotides (without reverse complement symmetry)

Gabriella Martini

2016-07-09

options(java.parameters = "-Xmx4000M")
library(SELEX)
library(SelexGLM)
library(grid)
workDir = "./cache/"
selex.config(workingDir=workDir, maxThreadNumber=4)

### LOCAL PATHS NEED TO BE RE-DEFINED TO RUN OFF OF MY COMPUTER
##################################################################
selexDir = "/Users/gabriella/Columbia/SELEX/"
rawdataDir = "/Users/gabriella/Columbia/rawdata/Mann/HM/"

# CLUSTER VERSIONS ARE COMMENTED OUT
#selexDir = "/vega/hblab/users/gdm2120/SELEX/SELEX/"
#rawdataDir = "/vega/hblab/projects/selex/rawdata/Mann/hm/"
##################################################################
saveDir = "gabriella/SelexGLMtest/NullNsetFixedValues/"
dir.create(file.path(selexDir, saveDir), showWarnings = FALSE, recursive = TRUE)


shapeTable = read.table(paste(selexDir, "gabriella/ShapeParamData/ShapeTableOrthogonal.txt", sep = ""), sep = "\t",
                        stringsAsFactors = FALSE)
ST = shapeTable[,c(1, 14:19)]
colnames(ST) = c("Sequence", "MGW", "ProT", "HelTA",
                 "HelTB", "RollA", "RollB")

selex.defineSample('r0',
                   paste(rawdataDir, "exp6/mplex1.0b.mplex2.0b.fastq.gz", sep = ""),
                   'm1r0',
                   0, 16, 'TGG', 'CCAGCTG')

selex.defineSample('r0',
                   paste(rawdataDir, "exp6/mplex1.0b.mplex2.0b.fastq.gz", sep = ""),
                   'm2r0',
                   0, 16, 'TGG', 'CCACGTC')



selex.defineSample('Ubx4a.R2',
                   paste(rawdataDir, "exp4/exdUbxiva.exdAntp.L.2.fastq.gz", sep = ""),
                   'HM.Ubx4a.Exd',
                   2, 16, 'TGG', 'CCAGCTG')

selex.defineSample('Ubx4a.R3',
                   paste(rawdataDir,"exp4/exdUbxiva.exdAntp.L.3.fastq.gz", sep = ""),
                   'HM.Ubx4a.Exd',
                   3, 16, 'TGG', 'CCAGCTG')




r0.train = selex.sample(seqName = 'r0', sampleName='m1r0', round = 0)
r0.test = selex.sample(seqName = 'r0', sampleName='m2r0', round = 0)
dataSample = selex.sample(seqName = 'Ubx4a.R2', sampleName = 'HM.Ubx4a.Exd', round = 2)

# MARKOV MODEL BUILT
kmax = selex.kmax(sample = r0.test)
# Train Markov model on Hm 16bp library Round 0 data
mm = selex.mm(sample = r0.train, order = NA, crossValidationSample =r0.test, Kmax = kmax, mmMethod = "TRANSITION")
mmscores = selex.mmSummary(sample = r0.train)
ido = which(mmscores$R==max(mmscores$R))
mm.order = mmscores$Order[ido]

libLen = as.numeric(as.character(selex.getAttributes(dataSample)$VariableRegionLength))


# For the sake of previous analysis on the Hox data used in this example, I will use kLen = 12 as my k-mer length, even though kLen identified through the information gain analysis has kLen = 13.
kLen = 12

#data.probeCounts = getProbeCounts(dataSample, markovModel = mm)
#save(data.probeCounts, file = paste(selexDir, saveDir, "/data.probeCounts.RData", sep = ""))
load(file = paste(selexDir, saveDir, "/data.probeCounts.RData", sep = ""))
#data.kmerTable = getKmerCountAffinities(dataSample, k = kLen, minCount = 100, markovModel = mm)
#save(data.kmerTable, file = paste(selexDir, saveDir, "/data.kmerTable.RData", sep = ""))
load(file = paste(selexDir, saveDir, "/data.kmerTable.RData", sep = ""))
DummyModelTest = model(name = "HM-Exd-Ubx4a R2 Nucleotide+Shape Model",
                varRegLen = libLen,
                leftFixedSeq =  "GTTCAGAGTTCTACAGTCCGACGATCTGG", 
                rightFixedSeq ="CCAGCTGTCGTATGCCGTCTTCTGCTTG", 
                consensusSeq = "NTGAYNNAYNNN",
                affinityType = "AffinitySym",
                leftFixedSeqOverlap = 5,
                minAffinity = 0.00,
                missingValueSuppression = 1,
                minSeedValue = .01, 
                upFootprintExtend = 4,
                confidenceLevel = .95, 
                verbose = FALSE,
                includeShape = TRUE,
                shapeTable = ST,
                shapeParamsUsed = list(c("MGW", "HelT", "Roll", "ProT")),
                rounds = list(c(2)),
                rcSymmetric = FALSE)

# Add seed model
seedMat = seedTable2psam(DummyModelTest, data.kmerTable)

# Inputs about library are data specific 
ModelTest = model(name = "HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model",
                varRegLen = libLen,
                leftFixedSeq =  "GTTCAGAGTTCTACAGTCCGACGATCTGG", 
                rightFixedSeq ="CCAGCTGTCGTATGCCGTCTTCTGCTTG", 
                consensusSeq = "NTGAYNNAYNNN",
                affinityType = "AffinitySym",
                leftFixedSeqOverlap = 5,
                minAffinity = 0.00,
                missingValueSuppression = 1,
                minSeedValue = .01, 
                upFootprintExtend = 4,
                confidenceLevel = .95, 
                verbose = FALSE,
                includeShape = TRUE,
                shapeTable = ST,
                shapeParamsUsed = list(c("MGW", "HelT", "Roll", "ProT")),
                rounds = list(c(2)),
                rcSymmetric = FALSE,
                N.set = c(0),
                N.values = seedMat,
                useFixedValuesOffset.N = TRUE)



getFeatureDesign(ModelTest)
## Feature design for object of class 'model'
## 
## seedLen:  12 
## upFootprintExtend:  4 
## downFootprintExtend:  4 
## rcSymmetric:  FALSE 
## 
## Slot "N": 
## N.upFootprintExtend:  0 
## N.downFootprintExtend:  0 
## N.set:  0 
## Number of previous iterations:  0 
## 
## Slot "Intercept": 
## Number of Views per Strand of DNA: 7
## Number of Rounds: 1 (2)
## Number of previous iterations: 0
## 
## Slot "Shape": 
## ShapeParamsUsed:  HelT MGW ProT Roll 
## Shape.upFootprintExtend:  4 
## Shape.downFootprintExtend:  4 
## Shape.set:  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
## Number of previous iterations:  0
print(getValues(getN(ModelTest)))
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
plot(ModelTest@features@N, Ntitle = "HM-Ubx4a-Exd R2 Shape Only\n Nucleotide Seeding Model", ddG = TRUE)

Next we score the probes using topModelMatch

sample1 = sample(nrow(data.probeCounts), 1000000)
data = data.probeCounts[sample1, ]
#data = data.probeCounts
data = topModelMatch(data, ModelTest)
# Uses aligned probes to build design matrix
data = addDesignMatrix(data, ModelTest)
if (nrow(data) > 0) {
  designMatrixSummary = getDesignMatrix(ModelTest, data)
  print("Round summary: ")
  print (designMatrixSummary$Round)
  print("Mono-nucleotide summary: ")
  print (designMatrixSummary$N)
  print("View/strand orientation summary: ")
  print (designMatrixSummary$Intercept)
  # # Constructs regression expression with independent features using design matrix
  regressionFormula = updatedRegressionFormula(data, ModelTest)
  print("Regression Formula: ")
  print (regressionFormula)
  fit = glm(regressionFormula, 
            data=data, 
            family = poisson(link="log"))
  summary(fit)
  ModelTest = addNewBetas(ModelTest, data, fit)
  # # Nucleotide Features after first round of fitting
  summary(ModelTest)
  vPheight = verticalPlot_height(ModelTest)
  pM <- plot(ModelTest, plotTitle = "HM-Ubx4a-Exd R2 Shape + Fixed Nucleotide Fit", Nplot.ddG = TRUE, verticalPlots = TRUE)
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.pdf", sep = ""), height = vPheight, width = 6)
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.",1, ".pdf", sep = ""), height = vPheight, width = 6)
}
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 793246 793246
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  49753  81950  74909  67627  68262  68851  81749      493101
## Strand.R  36973  49961  47623  36520  37950  41232  49886      300145
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 24.33279
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02400017
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1             2            3           4
## Shape.HelTA -0.03746092  0.0002531573 -0.032989236 -0.07514097
## Shape.HelTB -0.03370836 -0.0090293852  0.012732113  0.11392973
## Shape.MGW   -0.21875748 -0.0950075628 -0.162591784 -0.13876255
## Shape.ProT   0.02036645 -0.0115209171  0.006479179 -0.01889141
## Shape.RollA -0.01418076 -0.0042957332  0.017050645 -0.01041439
## Shape.RollB  0.02852034  0.0009889512  0.015951726  0.04660905
##                         5            6           7           8          9
## Shape.HelTA -0.1030211237  0.002361495  0.18947924 -0.03923569  1.1178395
## Shape.HelTB  0.0002378051 -0.050105418 -0.13784881 -0.86379867 -0.1211715
## Shape.MGW    0.0564736141 -0.239366517  0.53181284 -0.93948709  2.0503362
## Shape.ProT  -0.0107679217  0.072565934 -0.03031325  0.04926943 -0.1842770
## Shape.RollA -0.0300944234  0.088090871  0.10501400  0.30787816  0.2729947
## Shape.RollB -0.0388980493 -0.025211914 -0.36786946 -0.32391041 -0.4400403
##                      10          11          12          13           14
## Shape.HelTA  0.23075175  0.74437573 -0.50670047  0.37116036  0.108963064
## Shape.HelTB -1.12609988  0.50703890 -0.04346978 -0.06097452 -0.142001251
## Shape.MGW   -4.55601215 -1.08441015 -1.26399274  0.75370596 -0.296715985
## Shape.ProT  -0.04834123  0.16692643  0.35011887 -0.22547320  0.005039905
## Shape.RollA  1.01343765  0.21425291 -0.03446783 -0.06334932  0.096017943
## Shape.RollB -0.02941537  0.03678129  0.34948559  0.01697440  0.026258278
##                      15          16           17           18
## Shape.HelTA  0.21006261 -0.07221152  0.063813163  0.029989420
## Shape.HelTB  0.00476564 -0.13985032 -0.088949986 -0.012623365
## Shape.MGW   -0.09046836 -0.13056265 -0.047265430 -0.039257022
## Shape.ProT   0.06351138 -0.02591270 -0.005424187 -0.008713411
## Shape.RollA  0.06867568  0.06556929  0.056508759  0.027923863
## Shape.RollB -0.02990179 -0.04380611 -0.034459202  0.004689098
##                        19            20
## Shape.HelTA -0.0247809322  0.0084544987
## Shape.HelTB -0.0311257476  0.0071018889
## Shape.MGW   -0.2222428997 -0.2465112395
## Shape.ProT  -0.0005381776  0.0263216554
## Shape.RollA  0.0134781783  0.0785664463
## Shape.RollB -0.0614785641 -0.0006543709
## 
## Shape beta errors:
##                        1            2            3            4
## Shape.HelTA 0.0009711828 0.0018209529 0.0017775978 0.0016740761
## Shape.HelTB 0.0020018123 0.0019591067 0.0017119047 0.0023310164
## Shape.MGW   0.0042708932 0.0046066109 0.0041807629 0.0049653757
## Shape.ProT  0.0005369745 0.0005240759 0.0005059925 0.0005272984
## Shape.RollA 0.0006177989 0.0012393582 0.0011203142 0.0010881089
## Shape.RollB 0.0013333403 0.0011515305 0.0010711602 0.0011140045
##                        5           6           7           8           9
## Shape.HelTA 0.0024401315 0.002411310 0.004036881 0.009710546 0.026040078
## Shape.HelTB 0.0023932987 0.003037255 0.006358107 0.019239897 0.022849221
## Shape.MGW   0.0053530929 0.005142033 0.010069435 0.030091075 0.046307679
## Shape.ProT  0.0008751747 0.001632670 0.001682833 0.006457483 0.008485204
## Shape.RollA 0.0010695220 0.001731125 0.001452180 0.004315309 0.011050211
## Shape.RollB 0.0016189033 0.001343613 0.003975922 0.009742627 0.011883235
##                      10          11          12          13           14
## Shape.HelTA 0.017844153 0.022266688 0.014511153 0.009262620 0.0031376680
## Shape.HelTB 0.027893765 0.015285029 0.012827359 0.002938195 0.0024417461
## Shape.MGW   0.068969396 0.054563125 0.032262323 0.011819804 0.0051426916
## Shape.ProT  0.009802406 0.010053376 0.006730535 0.002016900 0.0008814845
## Shape.RollA 0.012660160 0.011176133 0.006901316 0.003726953 0.0012026247
## Shape.RollB 0.010781102 0.005962469 0.006025314 0.001371453 0.0009665863
##                       15           16           17           18
## Shape.HelTA 0.0023563665 0.0022548589 0.0018417403 0.0017711904
## Shape.HelTB 0.0022177690 0.0018480830 0.0016540096 0.0019324370
## Shape.MGW   0.0052229000 0.0048522671 0.0047395946 0.0044688061
## Shape.ProT  0.0006045072 0.0005161645 0.0005131484 0.0005322631
## Shape.RollA 0.0010430765 0.0012932645 0.0010504760 0.0011138504
## Shape.RollB 0.0013175143 0.0010676451 0.0011341796 0.0012316858
##                       19           20
## Shape.HelTA 0.0021140232 0.0021350354
## Shape.HelTB 0.0019906752 0.0011322311
## Shape.MGW   0.0049578168 0.0047471026
## Shape.ProT  0.0005617729 0.0005723985
## Shape.RollA 0.0012910039 0.0014852900
## Shape.RollB 0.0013971447 0.0007352046

some text

data = data.probeCounts[sample1, ]
#data = data.probeCounts
data.nrow = nrow(data)
data = topModelMatch(data, ModelTest)
data = addDesignMatrix(data, ModelTest)
if (nrow(data) > 0) {
  designMatrixSummary.v2 = getDesignMatrix(ModelTest, data)
  if ((all(designMatrixSummary.v2$N == designMatrixSummary$N)) & (all(designMatrixSummary.v2$Round == designMatrixSummary$Round)) & (all(designMatrixSummary.v2$Intercept == designMatrixSummary$Intercept)))  {
    print ("Stability Reached")
  }
} 
## No nucleotides included in fit.
for (i in 2:20) {
  if (nrow(data) == 0) {
    break
  } else if ((all(designMatrixSummary.v2$N == designMatrixSummary$N)) & (all(designMatrixSummary.v2$Round == designMatrixSummary$Round)) & (all(designMatrixSummary.v2$Intercept == designMatrixSummary$Intercept)))  {
    break
  }
  data.nrow = nrow(data)
  print (paste("i =",i))
  
  designMatrixSummary = getDesignMatrix(ModelTest, data)
  print("Round summary: ")
  print (designMatrixSummary$Round)
  print("Mono-nucleotide summary: ")
  print (designMatrixSummary$N)
  print("View/strand orientation summary: ")
  print (designMatrixSummary$Intercept)
  # # Constructs regression expression with independent features using design matrix
  regressionFormula = updatedRegressionFormula(data, ModelTest)
  print("Regression Formula: ")
  print (regressionFormula)
  fit = glm(regressionFormula, 
            data=data, 
            family = poisson(link="log"))
  summary(fit)
  ModelTest = addNewBetas(ModelTest, data, fit)
  # # Nucleotide Features after first round of fitting
  summary(ModelTest)
  pM <- plot(ModelTest, plotTitle = "HM-Ubx4a-Exd R2 Shape+Fixed Nucleotide Fit", Nplot.ddG = TRUE, verticalPlots = TRUE)
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.pdf", sep = ""), height = vPheight, width = 6)
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.",i, ".pdf", sep = ""), height = vPheight, width = 6)
  data = topModelMatch(data, ModelTest)
  data = addDesignMatrix(data, ModelTest)
  print(paste("Number of Observations in Design Matrix: ",nrow(data), sep = ""))
  if (nrow(data) > 0) {
    designMatrixSummary.v2 = getDesignMatrix(ModelTest, data)
    if ((all(designMatrixSummary.v2$N == designMatrixSummary$N)) & (all(designMatrixSummary.v2$Round == designMatrixSummary$Round)) & (all(designMatrixSummary.v2$Intercept == designMatrixSummary$Intercept)))  {
      print (paste("Stability Reached after ", i, " iterations.", sep = ""))
      break
    }
  } else  {
    print (paste("Algorithm failed to converge: No probes meet the confidence level requirement (Confidence Level:", ModelTest@confidenceLevel, ")", sep = ""))
  }
}
## [1] "i = 2"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 768459 768459
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  49067  82236  75900  64918  64079  63485  75387      475072
## Strand.R  37178  50265  49338  35247  36448  38964  45947      293387
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 24.05005
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02615828
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03643018 -0.001290056 -0.031698817 -0.07820101 -0.099956682
## Shape.HelTB -0.03129673 -0.011824191  0.015140795  0.11376581  0.002962916
## Shape.MGW   -0.21863192 -0.085867542 -0.182201247 -0.13875834  0.055401861
## Shape.ProT   0.02122166 -0.011898014  0.005897535 -0.01729346 -0.010515994
## Shape.RollA -0.01447388 -0.004567993  0.016882668 -0.01205879 -0.028615335
## Shape.RollB  0.02926535  0.001847926  0.016358976  0.04974554 -0.037142648
##                        6           7           8          9          10
## Shape.HelTA  0.006927836  0.19975369  0.02524067  1.1464976  0.24377203
## Shape.HelTB -0.055898748 -0.14210193 -0.82411768 -0.1633327 -1.25218351
## Shape.MGW   -0.243550192  0.52641313 -0.85337474  2.1426196 -4.80595956
## Shape.ProT   0.075642125 -0.03526279  0.07143117 -0.1598602 -0.15903124
## Shape.RollA  0.091604660  0.11001941  0.30748434  0.3088950  1.14446305
## Shape.RollB -0.025141647 -0.36612945 -0.33031887 -0.5201987 -0.02169723
##                      11           12          13           14           15
## Shape.HelTA  0.59741150 -0.380460127  0.44805681  0.086460373  0.229908960
## Shape.HelTB  0.24391066 -0.080790846 -0.04784654 -0.159304521  0.002120605
## Shape.MGW   -1.48474149 -1.093903707  0.85890750 -0.286727915 -0.065313173
## Shape.ProT   0.06640494  0.337170818 -0.20462170 -0.003142655  0.065456603
## Shape.RollA  0.19017931 -0.001730494 -0.06435956  0.085497265  0.070720334
## Shape.RollB -0.01115574  0.368598411  0.01600001  0.023088231 -0.034720633
##                      16           17           18           19
## Shape.HelTA -0.06801165  0.068164199  0.031121271 -0.025668103
## Shape.HelTB -0.14566366 -0.089564325 -0.011431469 -0.029960788
## Shape.MGW   -0.13855358 -0.034859919 -0.038080325 -0.219448106
## Shape.ProT  -0.02584483 -0.005231356 -0.008530570 -0.001355594
## Shape.RollA  0.06876528  0.055054456  0.025925151  0.013700237
## Shape.RollB -0.04571863 -0.033270290  0.004137815 -0.060393005
##                       20
## Shape.HelTA  0.006694108
## Shape.HelTB  0.005697098
## Shape.MGW   -0.248186796
## Shape.ProT   0.025511499
## Shape.RollA  0.077333500
## Shape.RollB -0.001365568
## 
## Shape beta errors:
##                        1            2            3            4
## Shape.HelTA 0.0009915010 0.0018636412 0.0018114736 0.0016977715
## Shape.HelTB 0.0020482752 0.0020018103 0.0017463277 0.0023763910
## Shape.MGW   0.0043365271 0.0047072365 0.0042896230 0.0050955925
## Shape.ProT  0.0005485294 0.0005367784 0.0005209751 0.0005348532
## Shape.RollA 0.0006293916 0.0012743570 0.0011435098 0.0011388514
## Shape.RollB 0.0013663556 0.0011782681 0.0011173523 0.0011355038
##                        5           6           7           8          9
## Shape.HelTA 0.0024938291 0.002432122 0.004069490 0.009821584 0.02634411
## Shape.HelTB 0.0024368446 0.003082878 0.006328484 0.019500797 0.02317871
## Shape.MGW   0.0054788989 0.005186565 0.010160288 0.029716344 0.04610047
## Shape.ProT  0.0008940363 0.001631965 0.001688765 0.006588865 0.00840575
## Shape.RollA 0.0010941376 0.001778395 0.001460731 0.004201626 0.01129389
## Shape.RollB 0.0016585141 0.001350276 0.003959711 0.009973693 0.01231997
##                      10          11          12          13           14
## Shape.HelTA 0.017716368 0.023213609 0.014324155 0.009544813 0.0032581224
## Shape.HelTB 0.029206211 0.015607591 0.013438064 0.003051233 0.0025715109
## Shape.MGW   0.069430438 0.053855536 0.032190271 0.012342803 0.0052498549
## Shape.ProT  0.009976705 0.010380245 0.007064689 0.002014434 0.0009163353
## Shape.RollA 0.012776466 0.011607335 0.007380161 0.003787108 0.0012401197
## Shape.RollB 0.011012339 0.006373461 0.006307773 0.001405536 0.0009888461
##                      15          16           17           18           19
## Shape.HelTA 0.002461588 0.002306062 0.0018594650 0.0017901494 0.0021342490
## Shape.HelTB 0.002271414 0.001869713 0.0016706027 0.0019487582 0.0019993228
## Shape.MGW   0.005355611 0.004934159 0.0048017090 0.0045239125 0.0050088722
## Shape.ProT  0.000625863 0.000526460 0.0005203769 0.0005378573 0.0005669198
## Shape.RollA 0.001066312 0.001319509 0.0010675342 0.0011248293 0.0013023230
## Shape.RollB 0.001345720 0.001086453 0.0011449926 0.0012443078 0.0014087950
##                       20
## Shape.HelTA 0.0021483933
## Shape.HelTB 0.0011427548
## Shape.MGW   0.0047924981
## Shape.ProT  0.0005762933
## Shape.RollA 0.0014958574
## Shape.RollB 0.0007416765
## 
## [1] "Number of Observations in Design Matrix: 750922"
## No nucleotides included in fit.
## [1] "i = 3"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 750922 750922
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48394  81230  75029  62696  62048  61391  73195      463983
## Strand.R  36672  49749  48850  33959  35323  37824  44562      286939
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.93095
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02761186
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03616809 -0.003350072 -0.031665753 -0.07946916 -0.103196291
## Shape.HelTB -0.02847831 -0.011109010  0.015425272  0.11623209  0.002560043
## Shape.MGW   -0.22228612 -0.080949420 -0.193235211 -0.13647170  0.049818714
## Shape.ProT   0.02115149 -0.011406991  0.005695071 -0.01680205 -0.011219517
## Shape.RollA -0.01459903 -0.005805323  0.016328772 -0.01387110 -0.030309042
## Shape.RollB  0.03078584  0.003758801  0.017661178  0.05223751 -0.033235437
##                        6          7           8          9           10
## Shape.HelTA  0.004775722  0.1995940  0.03155384  1.1378859  0.244930245
## Shape.HelTB -0.055716819 -0.1392699 -0.81205807 -0.1958238 -1.339110734
## Shape.MGW   -0.241452941  0.5225987 -0.85304487  2.2248033 -4.959085001
## Shape.ProT   0.073581660 -0.0336298  0.07034404 -0.1572454 -0.193294850
## Shape.RollA  0.087459260  0.1087862  0.30554449  0.3007525  1.189492649
## Shape.RollB -0.023050522 -0.3611582 -0.32096128 -0.5585895 -0.004545362
##                      11           12          13           14
## Shape.HelTA  0.60346038 -0.389896481  0.44478703  0.084346165
## Shape.HelTB  0.19612319 -0.079122479 -0.04361805 -0.159050557
## Shape.MGW   -1.56915599 -1.050757787  0.85639429 -0.289430781
## Shape.ProT   0.03780714  0.344667499 -0.20295657 -0.004214218
## Shape.RollA  0.17392518  0.001775349 -0.06324378  0.085190466
## Shape.RollB -0.02451603  0.365081978  0.01521152  0.022456996
##                        15          16           17           18
## Shape.HelTA  0.2319080816 -0.06686265  0.069160723  0.031689749
## Shape.HelTB  0.0006179605 -0.14714439 -0.089537843 -0.010877044
## Shape.MGW   -0.0636627867 -0.13895484 -0.035864837 -0.038953678
## Shape.ProT   0.0662379341 -0.02620615 -0.004777934 -0.008361491
## Shape.RollA  0.0725880121  0.06995711  0.055215471  0.025672808
## Shape.RollB -0.0366257917 -0.04632839 -0.032980906  0.004058252
##                       19           20
## Shape.HelTA -0.026198411  0.006704513
## Shape.HelTB -0.030168682  0.005466951
## Shape.MGW   -0.216728758 -0.247211971
## Shape.ProT  -0.001777072  0.025302340
## Shape.RollA  0.013904996  0.076326663
## Shape.RollB -0.059968214 -0.001605061
## 
## Shape beta errors:
##                        1            2           3            4
## Shape.HelTA 0.0010010020 0.0018810301 0.001828598 0.0017078696
## Shape.HelTB 0.0020686515 0.0020219242 0.001760030 0.0023985030
## Shape.MGW   0.0043671445 0.0047495517 0.004336471 0.0051590637
## Shape.ProT  0.0005539226 0.0005436991 0.000528457 0.0005395978
## Shape.RollA 0.0006347153 0.0012887321 0.001152631 0.0011571448
## Shape.RollB 0.0013806939 0.0011885774 0.001133708 0.0011517838
##                        5           6           7           8           9
## Shape.HelTA 0.0025204871 0.002449154 0.004092798 0.009949315 0.026891705
## Shape.HelTB 0.0024601621 0.003108030 0.006352871 0.020035097 0.023692904
## Shape.MGW   0.0055416732 0.005232003 0.010219288 0.030183932 0.046954010
## Shape.ProT  0.0009028399 0.001642813 0.001705098 0.006713094 0.008548515
## Shape.RollA 0.0011121507 0.001799337 0.001470820 0.004229854 0.011481570
## Shape.RollB 0.0016787699 0.001362290 0.003981508 0.010149177 0.012694382
##                     10          11          12          13           14
## Shape.HelTA 0.01802508 0.023930404 0.014593349 0.009778500 0.0033144985
## Shape.HelTB 0.03027874 0.016321954 0.013801381 0.003115445 0.0026113392
## Shape.MGW   0.07219415 0.055707824 0.033290629 0.012486750 0.0053115156
## Shape.ProT  0.01025276 0.010743054 0.007398948 0.002070662 0.0009313542
## Shape.RollA 0.01318869 0.011907307 0.007567474 0.003870031 0.0012574375
## Shape.RollB 0.01137035 0.006609293 0.006450461 0.001427114 0.0009992646
##                       15           16           17           18
## Shape.HelTA 0.0024955658 0.0023261249 0.0018702819 0.0017994321
## Shape.HelTB 0.0022952856 0.0018813345 0.0016794471 0.0019567700
## Shape.MGW   0.0054102999 0.0049731139 0.0048339682 0.0045498564
## Shape.ProT  0.0006344596 0.0005318664 0.0005235854 0.0005406376
## Shape.RollA 0.0010756596 0.0013313866 0.0010747549 0.0011296572
## Shape.RollB 0.0013589362 0.0010942485 0.0011499936 0.0012496876
##                       19           20
## Shape.HelTA 0.0021440098 0.0021558116
## Shape.HelTB 0.0020047779 0.0011473724
## Shape.MGW   0.0050335900 0.0048161076
## Shape.ProT  0.0005697233 0.0005781755
## Shape.RollA 0.0013072825 0.0015014904
## Shape.RollB 0.0014142953 0.0007448395
## 
## [1] "Number of Observations in Design Matrix: 747988"
## No nucleotides included in fit.
## [1] "i = 4"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 747988 747988
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48258  81017  74829  62379  61742  61059  72834      462118
## Strand.R  36553  49604  48729  33788  35189  37665  44342      285870
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.87552
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02808567
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03604888 -0.003610380 -0.031648790 -0.07958083 -0.103538311
## Shape.HelTB -0.02825006 -0.011228867  0.015473593  0.11623002  0.001999393
## Shape.MGW   -0.22242614 -0.079846256 -0.193783281 -0.13611872  0.050630921
## Shape.ProT   0.02113536 -0.011508557  0.005720382 -0.01686676 -0.011439669
## Shape.RollA -0.01466469 -0.006134530  0.016194592 -0.01412863 -0.030502996
## Shape.RollB  0.03102631  0.003856484  0.017878549  0.05223859 -0.033418802
##                        6           7           8          9           10
## Shape.HelTA  0.004991653  0.19960843  0.03506486  1.1247848  0.247148802
## Shape.HelTB -0.056083749 -0.13865362 -0.79876312 -0.2126969 -1.383243351
## Shape.MGW   -0.240492262  0.52257572 -0.84430143  2.2571653 -5.023645481
## Shape.ProT   0.073336678 -0.03313978  0.07020707 -0.1578136 -0.210029284
## Shape.RollA  0.087187344  0.10838977  0.30483348  0.2970484  1.211372843
## Shape.RollB -0.023040441 -0.36024727 -0.31564612 -0.5778074 -0.001306534
##                      11           12          13           14
## Shape.HelTA  0.61850518 -0.394045844  0.43926833  0.084938693
## Shape.HelTB  0.17675955 -0.075222054 -0.04221757 -0.158198426
## Shape.MGW   -1.61985463 -1.037676019  0.85304404 -0.289297786
## Shape.ProT   0.03175034  0.350986188 -0.20383508 -0.004290679
## Shape.RollA  0.17349573  0.003662459 -0.06355349  0.084985582
## Shape.RollB -0.03053753  0.362591800  0.01539545  0.022602886
##                        15          16           17           18
## Shape.HelTA  0.2318502257 -0.06677654  0.069572728  0.031662135
## Shape.HelTB  0.0006423587 -0.14742513 -0.089557595 -0.010934502
## Shape.MGW   -0.0633145150 -0.13942482 -0.035273612 -0.038823993
## Shape.ProT   0.0665697267 -0.02632624 -0.004734692 -0.008350689
## Shape.RollA  0.0728477526  0.07012184  0.055442071  0.025626349
## Shape.RollB -0.0368793701 -0.04659658 -0.033004451  0.004020278
##                       19           20
## Shape.HelTA -0.026099880  0.006807112
## Shape.HelTB -0.030216016  0.005447656
## Shape.MGW   -0.216667381 -0.247603441
## Shape.ProT  -0.001788286  0.025289754
## Shape.RollA  0.013939615  0.076355440
## Shape.RollB -0.059999902 -0.001592329
## 
## Shape beta errors:
##                        1            2            3            4
## Shape.HelTA 0.0010022182 0.0018826657 0.0018315536 0.0017087351
## Shape.HelTB 0.0020706756 0.0020252893 0.0017611633 0.0024004843
## Shape.MGW   0.0043716554 0.0047545320 0.0043411158 0.0051657129
## Shape.ProT  0.0005544582 0.0005445239 0.0005290257 0.0005400585
## Shape.RollA 0.0006353650 0.0012904722 0.0011541372 0.0011595037
## Shape.RollB 0.0013826026 0.0011904029 0.0011359752 0.0011535549
##                        5           6           7           8           9
## Shape.HelTA 0.0025229093 0.002450967 0.004095364 0.009985386 0.027025142
## Shape.HelTB 0.0024627689 0.003111248 0.006355908 0.020185309 0.023854618
## Shape.MGW   0.0055486325 0.005237097 0.010228490 0.030334020 0.047150211
## Shape.ProT  0.0009039037 0.001644005 0.001708133 0.006749971 0.008581347
## Shape.RollA 0.0011137143 0.001801192 0.001472533 0.004237383 0.011517440
## Shape.RollB 0.0016799056 0.001363147 0.003985740 0.010196629 0.012821132
##                     10          11          12          13           14
## Shape.HelTA 0.01812392 0.024143799 0.014605584 0.009801884 0.0033194916
## Shape.HelTB 0.03063500 0.016450898 0.013860643 0.003123484 0.0026141855
## Shape.MGW   0.07295276 0.056295978 0.033377465 0.012504058 0.0053176524
## Shape.ProT  0.01035722 0.010872130 0.007445780 0.002076894 0.0009329524
## Shape.RollA 0.01331625 0.012026835 0.007591418 0.003877344 0.0012592568
## Shape.RollB 0.01149036 0.006667877 0.006467856 0.001429378 0.0010001330
##                       15           16          17          18           19
## Shape.HelTA 0.0024981958 0.0023282249 0.001871940 0.001799988 0.0021451891
## Shape.HelTB 0.0022979409 0.0018828033 0.001680062 0.001957723 0.0020055195
## Shape.MGW   0.0054145949 0.0049772372 0.004838065 0.004552657 0.0050360708
## Shape.ProT  0.0006353851 0.0005323095 0.000523972 0.000540884 0.0005700113
## Shape.RollA 0.0010766770 0.0013324593 0.001075674 0.001130242 0.0013079138
## Shape.RollB 0.0013601579 0.0010952418 0.001150710 0.001250386 0.0014148641
##                       20
## Shape.HelTA 0.0021567718
## Shape.HelTB 0.0011478681
## Shape.MGW   0.0048186510
## Shape.ProT  0.0005784224
## Shape.RollA 0.0015020294
## Shape.RollB 0.0007451698
## 
## [1] "Number of Observations in Design Matrix: 746868"
## No nucleotides included in fit.
## [1] "i = 5"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 746868 746868
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48220  80928  74734  62269  61613  60977  72706      461447
## Strand.R  36505  49538  48675  33710  35120  37607  44266      285421
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.85846
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02823645
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03599603 -0.003774652 -0.031546280 -0.07957877 -0.103729412
## Shape.HelTB -0.02805199 -0.011343620  0.015500539  0.11632212  0.001994883
## Shape.MGW   -0.22247888 -0.079700610 -0.193909508 -0.13557564  0.050414535
## Shape.ProT   0.02117882 -0.011508892  0.005705734 -0.01689663 -0.011428277
## Shape.RollA -0.01471400 -0.006193313  0.016110940 -0.01425299 -0.030479718
## Shape.RollB  0.03113676  0.003934140  0.017946245  0.05221749 -0.033474035
##                        6           7           8          9           10
## Shape.HelTA  0.005074011  0.19953905  0.03651721  1.1197280  0.247692872
## Shape.HelTB -0.056095902 -0.13868806 -0.79399892 -0.2186537 -1.396111742
## Shape.MGW   -0.240446584  0.52252102 -0.84044825  2.2633808 -5.036701355
## Shape.ProT   0.073242983 -0.03302089  0.07066010 -0.1585927 -0.216045013
## Shape.RollA  0.087251499  0.10828447  0.30446804  0.2967344  1.217618854
## Shape.RollB -0.023035923 -0.35993203 -0.31409941 -0.5837961 -0.001603101
##                      11           12          13           14
## Shape.HelTA  0.62226320 -0.395166747  0.43832762  0.085100633
## Shape.HelTB  0.16996014 -0.075628664 -0.04207534 -0.158114689
## Shape.MGW   -1.63884675 -1.031013856  0.85230250 -0.289594425
## Shape.ProT   0.03117524  0.351685864 -0.20399316 -0.004330527
## Shape.RollA  0.17372442  0.003106344 -0.06350192  0.084925593
## Shape.RollB -0.03173078  0.361415515  0.01540285  0.022673311
##                        15          16           17           18
## Shape.HelTA  0.2318921554 -0.06680623  0.069639119  0.031638281
## Shape.HelTB  0.0007016267 -0.14752414 -0.089527468 -0.010919860
## Shape.MGW   -0.0632743021 -0.13944904 -0.035033786 -0.038823862
## Shape.ProT   0.0666390229 -0.02635985 -0.004719146 -0.008376987
## Shape.RollA  0.0729140692  0.07016204  0.055494768  0.025618103
## Shape.RollB -0.0369501611 -0.04667955 -0.033031874  0.003988759
##                       19           20
## Shape.HelTA -0.026129461  0.006788004
## Shape.HelTB -0.030268292  0.005457298
## Shape.MGW   -0.216546042 -0.247442553
## Shape.ProT  -0.001793148  0.025254722
## Shape.RollA  0.013927743  0.076299369
## Shape.RollB -0.059995995 -0.001614792
## 
## Shape beta errors:
##                        1           2            3            4
## Shape.HelTA 0.0010026557 0.001883515 0.0018320255 0.0017090437
## Shape.HelTB 0.0020715026 0.002025902 0.0017616619 0.0024011966
## Shape.MGW   0.0043728828 0.004756339 0.0043426384 0.0051684204
## Shape.ProT  0.0005546545 0.000544835 0.0005292407 0.0005402352
## Shape.RollA 0.0006355344 0.001290933 0.0011545532 0.0011608601
## Shape.RollB 0.0013830031 0.001190826 0.0011371681 0.0011540279
##                        5           6           7           8           9
## Shape.HelTA 0.0025238495 0.002451621 0.004096162 0.009997339 0.027067739
## Shape.HelTB 0.0024638962 0.003112160 0.006357061 0.020237743 0.023903070
## Shape.MGW   0.0055511160 0.005238448 0.010231176 0.030384188 0.047201965
## Shape.ProT  0.0009043531 0.001644344 0.001708989 0.006761948 0.008587576
## Shape.RollA 0.0011142490 0.001801967 0.001473032 0.004240430 0.011528713
## Shape.RollB 0.0016804614 0.001363434 0.003986887 0.010213012 0.012860978
##                     10          11          12          13           14
## Shape.HelTA 0.01815277 0.024205466 0.014615769 0.009810116 0.0033210856
## Shape.HelTB 0.03073581 0.016505970 0.013885931 0.003126205 0.0026151938
## Shape.MGW   0.07316507 0.056485964 0.033428597 0.012510178 0.0053196889
## Shape.ProT  0.01039761 0.010908885 0.007464839 0.002079505 0.0009335003
## Shape.RollA 0.01335514 0.012066785 0.007601679 0.003879861 0.0012599042
## Shape.RollB 0.01152691 0.006685461 0.006475588 0.001430094 0.0010005107
##                       15           16           17           18
## Shape.HelTA 0.0024991207 0.0023286317 0.0018723344 0.0018002908
## Shape.HelTB 0.0022983950 0.0018832505 0.0016803429 0.0019579609
## Shape.MGW   0.0054161738 0.0049785438 0.0048389447 0.0045534118
## Shape.ProT  0.0006357672 0.0005324546 0.0005240916 0.0005409937
## Shape.RollA 0.0010769383 0.0013327957 0.0010758761 0.0011304663
## Shape.RollB 0.0013605083 0.0010954570 0.0011509070 0.0012505817
##                       19           20
## Shape.HelTA 0.0021455140 0.0021570864
## Shape.HelTB 0.0020058316 0.0011480315
## Shape.MGW   0.0050373337 0.0048198718
## Shape.ProT  0.0005700903 0.0005784905
## Shape.RollA 0.0013080931 0.0015022785
## Shape.RollB 0.0014151047 0.0007453224
## 
## [1] "Number of Observations in Design Matrix: 746542"
## No nucleotides included in fit.
## [1] "i = 6"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 746542 746542
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48204  80901  74709  62236  61576  60931  72668      461225
## Strand.R  36491  49527  48661  33691  35106  37591  44250      285317
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.85602
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02826774
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03593835 -0.003781234 -0.031484933 -0.07957320 -0.103800522
## Shape.HelTB -0.02805067 -0.011444879  0.015513648  0.11637793  0.001896824
## Shape.MGW   -0.22239073 -0.079411344 -0.194213331 -0.13540831  0.050527042
## Shape.ProT   0.02118862 -0.011520081  0.005721766 -0.01690167 -0.011466501
## Shape.RollA -0.01474062 -0.006239733  0.016125479 -0.01436326 -0.030506751
## Shape.RollB  0.03115936  0.003913302  0.018048942  0.05224210 -0.033497055
##                        6           7           8          9           10
## Shape.HelTA  0.005113101  0.19948862  0.03696942  1.1191219  0.247813048
## Shape.HelTB -0.056159020 -0.13870283 -0.79314680 -0.2194708 -1.398153668
## Shape.MGW   -0.240422238  0.52238982 -0.84031684  2.2659928 -5.037997035
## Shape.ProT   0.073262703 -0.03304338  0.07060548 -0.1583762 -0.217251449
## Shape.RollA  0.087202545  0.10822057  0.30457407  0.2963091  1.218562041
## Shape.RollB -0.022983807 -0.35989207 -0.31362606 -0.5848445 -0.001884658
##                      11           12          13           14
## Shape.HelTA  0.62365783 -0.394710693  0.43831509  0.085115435
## Shape.HelTB  0.16887800 -0.075306684 -0.04198087 -0.158085535
## Shape.MGW   -1.64197579 -1.028809633  0.85204252 -0.289659147
## Shape.ProT   0.03145668  0.352057918 -0.20405537 -0.004350426
## Shape.RollA  0.17427359  0.003239896 -0.06333717  0.084962474
## Shape.RollB -0.03215676  0.360932528  0.01539011  0.022692508
##                        15          16           17           18
## Shape.HelTA  0.2318685531 -0.06679737  0.069585221  0.031632741
## Shape.HelTB  0.0007309457 -0.14746925 -0.089537923 -0.010921482
## Shape.MGW   -0.0634821187 -0.13959756 -0.034901274 -0.038822421
## Shape.ProT   0.0666707575 -0.02635337 -0.004718494 -0.008383240
## Shape.RollA  0.0729412450  0.07018068  0.055483437  0.025633438
## Shape.RollB -0.0369235689 -0.04666546 -0.033050639  0.003967828
##                       19           20
## Shape.HelTA -0.026120582  0.006793185
## Shape.HelTB -0.030277041  0.005454399
## Shape.MGW   -0.216569929 -0.247307551
## Shape.ProT  -0.001793896  0.025244329
## Shape.RollA  0.013939205  0.076265551
## Shape.RollB -0.059980160 -0.001638261
## 
## Shape beta errors:
##                        1            2            3            4
## Shape.HelTA 0.0010028666 0.0018835627 0.0018322400 0.0017090468
## Shape.HelTB 0.0020717201 0.0020261964 0.0017618006 0.0024013248
## Shape.MGW   0.0043731325 0.0047569090 0.0043432095 0.0051687439
## Shape.ProT  0.0005546930 0.0005448795 0.0005293068 0.0005402645
## Shape.RollA 0.0006356581 0.0012911361 0.0011548108 0.0011611719
## Shape.RollB 0.0013832212 0.0011910664 0.0011375545 0.0011541359
##                        5           6           7           8           9
## Shape.HelTA 0.0025240344 0.002451777 0.004096414 0.009998832 0.027076714
## Shape.HelTB 0.0024641260 0.003112430 0.006357294 0.020245278 0.023912060
## Shape.MGW   0.0055516168 0.005238719 0.010231871 0.030392383 0.047215361
## Shape.ProT  0.0009044487 0.001644365 0.001709094 0.006763649 0.008590632
## Shape.RollA 0.0011143467 0.001802327 0.001473123 0.004240709 0.011530949
## Shape.RollB 0.0016806777 0.001363489 0.003987001 0.010215207 0.012868790
##                     10          11          12          13           14
## Shape.HelTA 0.01815878 0.024219725 0.014616916 0.009811238 0.0033214889
## Shape.HelTB 0.03075889 0.016514638 0.013890465 0.003126764 0.0026153319
## Shape.MGW   0.07321773 0.056530155 0.033435665 0.012511419 0.0053200397
## Shape.ProT  0.01041024 0.010920061 0.007467950 0.002080034 0.0009335797
## Shape.RollA 0.01336558 0.012077079 0.007603549 0.003880336 0.0012600341
## Shape.RollB 0.01153597 0.006689742 0.006476740 0.001430190 0.0010005964
##                       15           16           17           18
## Shape.HelTA 0.0024992675 0.0023287547 0.0018724389 0.0018003529
## Shape.HelTB 0.0022985740 0.0018833613 0.0016804230 0.0019580385
## Shape.MGW   0.0054164197 0.0049787996 0.0048390901 0.0045535484
## Shape.ProT  0.0006358326 0.0005324888 0.0005241148 0.0005410091
## Shape.RollA 0.0010770521 0.0013328475 0.0010759286 0.0011305076
## Shape.RollB 0.0013605625 0.0010955112 0.0011509498 0.0012506217
##                       19           20
## Shape.HelTA 0.0021456008 0.0021571949
## Shape.HelTB 0.0020059200 0.0011480760
## Shape.MGW   0.0050376021 0.0048201571
## Shape.ProT  0.0005701061 0.0005785264
## Shape.RollA 0.0013081210 0.0015023481
## Shape.RollB 0.0014151618 0.0007453539
## 
## [1] "Number of Observations in Design Matrix: 746480"
## No nucleotides included in fit.
## [1] "i = 7"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 746480 746480
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48203  80895  74704  62231  61575  60926  72659      461193
## Strand.R  36488  49522  48657  33685  35099  37589  44247      285287
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.85511
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02827511
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03595086 -0.003781679 -0.031484411 -0.07957910 -0.103808870
## Shape.HelTB -0.02805215 -0.011446468  0.015508879  0.11638104  0.001872506
## Shape.MGW   -0.22235832 -0.079408454 -0.194165207 -0.13538456  0.050537863
## Shape.ProT   0.02118338 -0.011521408  0.005719586 -0.01690625 -0.011476480
## Shape.RollA -0.01473941 -0.006245826  0.016120723 -0.01438057 -0.030509379
## Shape.RollB  0.03115437  0.003911047  0.018061798  0.05223617 -0.033498122
##                        6           7           8          9          10
## Shape.HelTA  0.005116961  0.19950845  0.03705487  1.1187106  0.24794569
## Shape.HelTB -0.056186892 -0.13866474 -0.79278889 -0.2198106 -1.39882260
## Shape.MGW   -0.240414666  0.52238323 -0.84008191  2.2670688 -5.03856756
## Shape.ProT   0.073263262 -0.03303088  0.07059709 -0.1583966 -0.21761145
## Shape.RollA  0.087192135  0.10821537  0.30456653  0.2961611  1.21906215
## Shape.RollB -0.022980849 -0.35987373 -0.31349560 -0.5853363 -0.00189337
##                      11           12          13           14
## Shape.HelTA  0.62357470 -0.395029775  0.43840112  0.085068711
## Shape.HelTB  0.16842582 -0.075585147 -0.04195881 -0.158268401
## Shape.MGW   -1.64363110 -1.027672819  0.85200882 -0.289681856
## Shape.ProT   0.03129664  0.351932990 -0.20403353 -0.004364134
## Shape.RollA  0.17419034  0.003092689 -0.06328424  0.084931888
## Shape.RollB -0.03217899  0.360711114  0.01539761  0.022681747
##                        15          16           17           18
## Shape.HelTA  0.2320342859 -0.06680821  0.069578511  0.031633948
## Shape.HelTB  0.0007261162 -0.14748643 -0.089534232 -0.010918301
## Shape.MGW   -0.0633254694 -0.13963970 -0.034935246 -0.038846380
## Shape.ProT   0.0666519597 -0.02634766 -0.004722324 -0.008382128
## Shape.RollA  0.0729470460  0.07019934  0.055491660  0.025635241
## Shape.RollB -0.0369496000 -0.04667513 -0.033049525  0.003970472
##                       19           20
## Shape.HelTA -0.026122535  0.006794554
## Shape.HelTB -0.030280811  0.005452516
## Shape.MGW   -0.216535978 -0.247302299
## Shape.ProT  -0.001791839  0.025242065
## Shape.RollA  0.013937214  0.076259766
## Shape.RollB -0.059978998 -0.001638196
## 
## Shape beta errors:
##                        1            2            3            4
## Shape.HelTA 0.0010029360 0.0018835826 0.0018322644 0.0017090722
## Shape.HelTB 0.0020717420 0.0020262339 0.0017618031 0.0024013296
## Shape.MGW   0.0043731381 0.0047569173 0.0043432962 0.0051688325
## Shape.ProT  0.0005546944 0.0005448863 0.0005293094 0.0005402766
## Shape.RollA 0.0006356758 0.0012911988 0.0011548499 0.0011613247
## Shape.RollB 0.0013832519 0.0011910825 0.0011377015 0.0011541422
##                        5           6           7           8           9
## Shape.HelTA 0.0025240525 0.002451774 0.004096415 0.009999162 0.027077534
## Shape.HelTB 0.0024641815 0.003112483 0.006357334 0.020247207 0.023913422
## Shape.MGW   0.0055516313 0.005238787 0.010231986 0.030393560 0.047216949
## Shape.ProT  0.0009044692 0.001644361 0.001709107 0.006764034 0.008590851
## Shape.RollA 0.0011143720 0.001802346 0.001473134 0.004240740 0.011531198
## Shape.RollB 0.0016806730 0.001363488 0.003987011 0.010215594 0.012870112
##                     10          11          12          13           14
## Shape.HelTA 0.01815897 0.024222900 0.014617079 0.009811692 0.0033215587
## Shape.HelTB 0.03076401 0.016518032 0.013891621 0.003126847 0.0026158153
## Shape.MGW   0.07322572 0.056538992 0.033439346 0.012511523 0.0053200803
## Shape.ProT  0.01041164 0.010920969 0.007469553 0.002080180 0.0009336034
## Shape.RollA 0.01336693 0.012078105 0.007604011 0.003880482 0.0012600764
## Shape.RollB 0.01153688 0.006690504 0.006477022 0.001430212 0.0010006097
##                       15           16           17           18
## Shape.HelTA 0.0024996378 0.0023287451 0.0018723942 0.0018003653
## Shape.HelTB 0.0022985710 0.0018833276 0.0016804294 0.0019580335
## Shape.MGW   0.0054166224 0.0049788069 0.0048391007 0.0045535604
## Shape.ProT  0.0006358738 0.0005324918 0.0005241195 0.0005410107
## Shape.RollA 0.0010770557 0.0013328611 0.0010759371 0.0011305116
## Shape.RollB 0.0013605805 0.0010955231 0.0011509506 0.0012506229
##                       19           20
## Shape.HelTA 0.0021455990 0.0021572104
## Shape.HelTB 0.0020059347 0.0011480772
## Shape.MGW   0.0050376212 0.0048201992
## Shape.ProT  0.0005701082 0.0005785277
## Shape.RollA 0.0013081216 0.0015023521
## Shape.RollB 0.0014151643 0.0007453653
## 
## [1] "Number of Observations in Design Matrix: 746452"
## No nucleotides included in fit.
## [1] "i = 8"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 746452 746452
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48203  80892  74703  62228  61573  60926  72654      461179
## Strand.R  36487  49519  48654  33684  35097  37587  44245      285273
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.85498
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02827586
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03595169 -0.003781179 -0.031490996 -0.07957966 -0.103807523
## Shape.HelTB -0.02805708 -0.011443637  0.015510384  0.11638151  0.001872686
## Shape.MGW   -0.22235777 -0.079419857 -0.194145553 -0.13538424  0.050519277
## Shape.ProT   0.02118253 -0.011522903  0.005719389 -0.01690639 -0.011477103
## Shape.RollA -0.01473972 -0.006247215  0.016119813 -0.01437964 -0.030508994
## Shape.RollB  0.03115686  0.003909504  0.018060674  0.05223613 -0.033492370
##                        6          7           8          9           10
## Shape.HelTA  0.005110127  0.1995242  0.03704131  1.1186853  0.247918100
## Shape.HelTB -0.056196347 -0.1386703 -0.79281593 -0.2198420 -1.398806842
## Shape.MGW   -0.240409626  0.5223577 -0.84006618  2.2669847 -5.038887074
## Shape.ProT   0.073262233 -0.0330264  0.07058726 -0.1584193 -0.217576586
## Shape.RollA  0.087187266  0.1082150  0.30455769  0.2961644  1.219057611
## Shape.RollB -0.022982376 -0.3598666 -0.31349783 -0.5853208 -0.001867679
##                      11           12          13           14
## Shape.HelTA  0.62343264 -0.394973227  0.43844583  0.085058522
## Shape.HelTB  0.16834807 -0.075518297 -0.04196733 -0.158276062
## Shape.MGW   -1.64324746 -1.028301629  0.85199480 -0.289684372
## Shape.ProT   0.03116730  0.351936458 -0.20401461 -0.004358556
## Shape.RollA  0.17416164  0.003220704 -0.06327556  0.084935378
## Shape.RollB -0.03223442  0.360861197  0.01540312  0.022681688
##                        15          16           17           18
## Shape.HelTA  0.2320392505 -0.06681504  0.069580589  0.031631671
## Shape.HelTB  0.0007387354 -0.14749015 -0.089532684 -0.010920571
## Shape.MGW   -0.0632914584 -0.13964446 -0.034948084 -0.038841598
## Shape.ProT   0.0666483385 -0.02634784 -0.004721294 -0.008383017
## Shape.RollA  0.0729418267  0.07019495  0.055490983  0.025630219
## Shape.RollB -0.0369470680 -0.04667374 -0.033043432  0.003970751
##                       19           20
## Shape.HelTA -0.026120169  0.006790360
## Shape.HelTB -0.030276955  0.005451704
## Shape.MGW   -0.216546059 -0.247296259
## Shape.ProT  -0.001790524  0.025241252
## Shape.RollA  0.013938217  0.076256855
## Shape.RollB -0.059975629 -0.001638830
## 
## Shape beta errors:
##                        1            2            3           4
## Shape.HelTA 0.0010029411 0.0018835866 0.0018322839 0.001709072
## Shape.HelTB 0.0020717410 0.0020262408 0.0017618032 0.002401327
## Shape.MGW   0.0043731381 0.0047569388 0.0043433261 0.005168831
## Shape.ProT  0.0005546948 0.0005448881 0.0005293101 0.000540276
## Shape.RollA 0.0006356767 0.0012912034 0.0011548520 0.001161326
## Shape.RollB 0.0013832621 0.0011910846 0.0011377023 0.001154143
##                        5           6           7           8          9
## Shape.HelTA 0.0025240512 0.002451791 0.004096442 0.009999257 0.02707777
## Shape.HelTB 0.0024641857 0.003112516 0.006357348 0.020247329 0.02391391
## Shape.MGW   0.0055516457 0.005238799 0.010232067 0.030394000 0.04721761
## Shape.ProT  0.0009044707 0.001644369 0.001709127 0.006764171 0.00859097
## Shape.RollA 0.0011143740 0.001802369 0.001473144 0.004240753 0.01153118
## Shape.RollB 0.0016806963 0.001363497 0.003987050 0.010215672 0.01287045
##                     10          11          12          13          14
## Shape.HelTA 0.01815946 0.024223371 0.014617341 0.009811851 0.003321574
## Shape.HelTB 0.03076482 0.016517578 0.013891652 0.003126883 0.002615843
## Shape.MGW   0.07322865 0.056540413 0.033439723 0.012511693 0.005320085
## Shape.ProT  0.01041120 0.010921206 0.007469739 0.002080179 0.000933609
## Shape.RollA 0.01336730 0.012078334 0.007604180 0.003880495 0.001260078
## Shape.RollB 0.01153746 0.006690834 0.006477151 0.001430221 0.001000610
##                       15           16           17           18
## Shape.HelTA 0.0024996541 0.0023287404 0.0018723960 0.0018003708
## Shape.HelTB 0.0022985872 0.0018833308 0.0016804312 0.0019580366
## Shape.MGW   0.0054166929 0.0049787982 0.0048391181 0.0045535975
## Shape.ProT  0.0006358772 0.0005324916 0.0005241203 0.0005410124
## Shape.RollA 0.0010770613 0.0013328651 0.0010759374 0.0011305257
## Shape.RollB 0.0013605824 0.0010955221 0.0011509618 0.0012506230
##                       19           20
## Shape.HelTA 0.0021456002 0.0021572128
## Shape.HelTB 0.0020059388 0.0011480778
## Shape.MGW   0.0050376395 0.0048202037
## Shape.ProT  0.0005701087 0.0005785284
## Shape.RollA 0.0013081225 0.0015023532
## Shape.RollB 0.0014151674 0.0007453670
## 
## [1] "Number of Observations in Design Matrix: 746449"
## No nucleotides included in fit.
## [1] "i = 9"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 746449 746449
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48203  80892  74703  62227  61573  60926  72652      461176
## Strand.R  36487  49519  48654  33684  35097  37587  44245      285273
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.85499
## 
## Intercept beta errors:
## Round.2:
## [1] 0.02827578
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4            5
## Shape.HelTA -0.03593990 -0.003767803 -0.031503339 -0.07958802 -0.103804849
## Shape.HelTB -0.02806980 -0.011446791  0.015505441  0.11638074  0.001890671
## Shape.MGW   -0.22234344 -0.079415200 -0.194136739 -0.13542246  0.050470818
## Shape.ProT   0.02118160 -0.011522978  0.005713997 -0.01690578 -0.011471938
## Shape.RollA -0.01474604 -0.006244600  0.016112340 -0.01437834 -0.030505112
## Shape.RollB  0.03115308  0.003914306  0.018056320  0.05224388 -0.033474862
##                        6           7           8          9           10
## Shape.HelTA  0.005090112  0.19951717  0.03704630  1.1186181  0.247919954
## Shape.HelTB -0.056189102 -0.13866178 -0.79278342 -0.2198778 -1.398836932
## Shape.MGW   -0.240440321  0.52235185 -0.84004288  2.2669863 -5.038897942
## Shape.ProT   0.073254659 -0.03301868  0.07057864 -0.1584302 -0.217595066
## Shape.RollA  0.087178518  0.10821081  0.30455178  0.2961432  1.219062628
## Shape.RollB -0.022974130 -0.35985140 -0.31347301 -0.5853308 -0.001885826
##                      11           12          13           14
## Shape.HelTA  0.62344203 -0.394980807  0.43847340  0.085065015
## Shape.HelTB  0.16835299 -0.075504764 -0.04196619 -0.158268138
## Shape.MGW   -1.64323819 -1.028291982  0.85205296 -0.289687090
## Shape.ProT   0.03117111  0.351935080 -0.20401144 -0.004356445
## Shape.RollA  0.17417171  0.003216656 -0.06327873  0.084935568
## Shape.RollB -0.03223430  0.360866491  0.01539720  0.022682639
##                        15          16           17           18
## Shape.HelTA  0.2320357014 -0.06681179  0.069585218  0.031630336
## Shape.HelTB  0.0007403126 -0.14749267 -0.089528315 -0.010917108
## Shape.MGW   -0.0632835890 -0.13965135 -0.034945080 -0.038833389
## Shape.ProT   0.0666496330 -0.02634694 -0.004719935 -0.008383159
## Shape.RollA  0.0729418291  0.07019409  0.055490671  0.025630709
## Shape.RollB -0.0369456750 -0.04667356 -0.033044076  0.003970501
##                       19           20
## Shape.HelTA -0.026124432  0.006796523
## Shape.HelTB -0.030277434  0.005454393
## Shape.MGW   -0.216539058 -0.247302431
## Shape.ProT  -0.001790427  0.025244084
## Shape.RollA  0.013938053  0.076260336
## Shape.RollB -0.059978608 -0.001638023
## 
## Shape beta errors:
##                        1            2            3           4
## Shape.HelTA 0.0010029602 0.0018835861 0.0018322920 0.001709082
## Shape.HelTB 0.0020717373 0.0020262360 0.0017618077 0.002401318
## Shape.MGW   0.0043731163 0.0047569198 0.0043433120 0.005168855
## Shape.ProT  0.0005546922 0.0005448872 0.0005293191 0.000540275
## Shape.RollA 0.0006356840 0.0012911971 0.0011548558 0.001161321
## Shape.RollB 0.0013832564 0.0011910829 0.0011376999 0.001154147
##                        5           6           7           8           9
## Shape.HelTA 0.0025240424 0.002451819 0.004096442 0.009999266 0.027077627
## Shape.HelTB 0.0024642048 0.003112521 0.006357353 0.020247212 0.023913799
## Shape.MGW   0.0055517044 0.005238817 0.010232062 0.030393996 0.047217683
## Shape.ProT  0.0009044744 0.001644379 0.001709134 0.006764164 0.008590922
## Shape.RollA 0.0011143725 0.001802375 0.001473142 0.004240775 0.011531129
## Shape.RollB 0.0016807245 0.001363503 0.003987043 0.010215645 0.012870455
##                     10          11          12          13           14
## Shape.HelTA 0.01815954 0.024223296 0.014617396 0.009811965 0.0033215783
## Shape.HelTB 0.03076474 0.016517675 0.013891816 0.003126883 0.0026158494
## Shape.MGW   0.07322863 0.056540294 0.033439847 0.012511746 0.0053200847
## Shape.ProT  0.01041129 0.010921268 0.007469793 0.002080237 0.0009336089
## Shape.RollA 0.01336729 0.012078424 0.007604194 0.003880516 0.0012600788
## Shape.RollB 0.01153755 0.006690841 0.006477167 0.001430221 0.0010006115
##                       15          16           17           18
## Shape.HelTA 0.0024996536 0.002328747 0.0018723912 0.0018003705
## Shape.HelTB 0.0022985926 0.001883326 0.0016804326 0.0019580349
## Shape.MGW   0.0054167074 0.004978804 0.0048391230 0.0045536088
## Shape.ProT  0.0006358781 0.000532491 0.0005241211 0.0005410123
## Shape.RollA 0.0010770626 0.001332866 0.0010759385 0.0011305271
## Shape.RollB 0.0013605839 0.001095523 0.0011509634 0.0012506237
##                       19           20
## Shape.HelTA 0.0021455996 0.0021572143
## Shape.HelTB 0.0020059374 0.0011480803
## Shape.MGW   0.0050376416 0.0048202040
## Shape.ProT  0.0005701089 0.0005785309
## Shape.RollA 0.0013081235 0.0015023555
## Shape.RollB 0.0014151690 0.0007453678
## 
## [1] "Number of Observations in Design Matrix: 746448"
## No nucleotides included in fit.
## [1] "i = 10"
## No nucleotides included in fit.
## [1] "Round summary: "
##            2  Total
## Round 746448 746448
## [1] "Mono-nucleotide summary: "
## <0 x 0 matrix>
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  48203  80892  74703  62227  61572  60926  72652      461175
## Strand.R  36487  49519  48654  33684  35097  37587  44245      285273
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+offset(fixedNddG)+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20"
## No nucleotides included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2 Shape+Fixed Nucleotides Model 
## Slot "varRegLen":  16 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATCTGG 
## Slot "rightFixedSeq":  CCAGCTGTCGTATGCCGTCTTCTGCTTG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.95 
## Slot "minAffinity":  0 
## Slot "missingValueSuppression":  1 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  12 
## Slot "consensusSeq":  [ACGT]TGA[CT][ACGT][ACGT]A[CT][ACGT][ACGT][ACGT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  20 
## 
## Fits a model of footprint length 20 for mono-nucleotide and shape features (shape = HelT, MGW, ProT, Roll)  with 7 view(s) per strand of DNA and 1 round(s) of data (round = 2) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+offset(fixedNddG)+Round.2+Shape.HelTA1+Shape.HelTB1+Shape.MGW1+Shape.ProT1+Shape.RollA1+Shape.RollB1+Shape.HelTA2+Shape.HelTB2+Shape.MGW2+Shape.ProT2+Shape.RollA2+Shape.RollB2+Shape.HelTA3+Shape.HelTB3+Shape.MGW3+Shape.ProT3+Shape.RollA3+Shape.RollB3+Shape.HelTA4+Shape.HelTB4+Shape.MGW4+Shape.ProT4+Shape.RollA4+Shape.RollB4+Shape.HelTA5+Shape.HelTB5+Shape.MGW5+Shape.ProT5+Shape.RollA5+Shape.RollB5+Shape.HelTA6+Shape.HelTB6+Shape.MGW6+Shape.ProT6+Shape.RollA6+Shape.RollB6+Shape.HelTA7+Shape.HelTB7+Shape.MGW7+Shape.ProT7+Shape.RollA7+Shape.RollB7+Shape.HelTA8+Shape.HelTB8+Shape.MGW8+Shape.ProT8+Shape.RollA8+Shape.RollB8+Shape.HelTA9+Shape.HelTB9+Shape.MGW9+Shape.ProT9+Shape.RollA9+Shape.RollB9+Shape.HelTA10+Shape.HelTB10+Shape.MGW10+Shape.ProT10+Shape.RollA10+Shape.RollB10+Shape.HelTA11+Shape.HelTB11+Shape.MGW11+Shape.ProT11+Shape.RollA11+Shape.RollB11+Shape.HelTA12+Shape.HelTB12+Shape.MGW12+Shape.ProT12+Shape.RollA12+Shape.RollB12+Shape.HelTA13+Shape.HelTB13+Shape.MGW13+Shape.ProT13+Shape.RollA13+Shape.RollB13+Shape.HelTA14+Shape.HelTB14+Shape.MGW14+Shape.ProT14+Shape.RollA14+Shape.RollB14+Shape.HelTA15+Shape.HelTB15+Shape.MGW15+Shape.ProT15+Shape.RollA15+Shape.RollB15+Shape.HelTA16+Shape.HelTB16+Shape.MGW16+Shape.ProT16+Shape.RollA16+Shape.RollB16+Shape.HelTA17+Shape.HelTB17+Shape.MGW17+Shape.ProT17+Shape.RollA17+Shape.RollB17+Shape.HelTA18+Shape.HelTB18+Shape.MGW18+Shape.ProT18+Shape.RollA18+Shape.RollB18+Shape.HelTA19+Shape.HelTB19+Shape.MGW19+Shape.ProT19+Shape.RollA19+Shape.RollB19+Shape.HelTA20+Shape.HelTB20+Shape.MGW20+Shape.ProT20+Shape.RollA20+Shape.RollB20 
## 
## Slot "shapeParamsUsed[[1]]":  HelT MGW ProT Roll 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 1 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##     1 2 3 4          5          6          7         8         9        10
## N.A 0 0 0 0  0.0000000 -0.8340377 -0.6171102  0.000000 -1.360965 -1.476628
## N.C 0 0 0 0 -0.8162560 -1.8500362 -3.1650820 -2.675131 -1.992603 -2.448111
## N.G 0 0 0 0 -0.2525938 -2.1521858  0.0000000 -2.618543 -1.264517 -2.484039
## N.T 0 0 0 0 -0.4154319  0.0000000 -1.3143951 -2.908717  0.000000  0.000000
##            11        12        13          14         15         16 17 18
## N.A -1.118790  0.000000 -2.022527 -0.86831649  0.0000000 -0.7152829  0  0
## N.C -2.174582 -3.392451 -1.355055 -1.05294403 -1.6266289  0.0000000  0  0
## N.G -1.362605 -2.603949 -1.716115 -0.02638645 -0.0963874 -0.3890593  0  0
## N.T  0.000000 -3.561304  0.000000  0.00000000 -1.0818102 -0.2918482  0  0
##     19 20
## N.A  0  0
## N.C  0  0
## N.G  0  0
## N.T  0  0
## 
## Nucleotide beta errors:
##     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## N.A 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.C 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.G 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## N.T 0 0 0 0 0 0 0 0 0  0  0  0  0  0  0  0  0  0  0  0
## 
## 
## An object of class 'Intercept'
## Fits intercept(s) for 1 round(s) (round = 2).
## Intercept beta values:
## Round.2:
## [1] 23.85503
## 
## Intercept beta errors:
## Round.2:
## [1] 0.0282758
## 
## 
## 
## An object of class 'Shape'
## Fits 120 shape coefficients for 6 kinds of shape parameter(s) (shape = HelT, MGW, ProT, Roll) for a feature model of length 20.
## Shape beta values:
##                       1            2            3           4           5
## Shape.HelTA -0.03594000 -0.003767731 -0.031503280 -0.07958798 -0.10380517
## Shape.HelTB -0.02807006 -0.011446800  0.015505379  0.11638101  0.00189007
## Shape.MGW   -0.22234310 -0.079414876 -0.194136806 -0.13542301  0.05047084
## Shape.ProT   0.02118147 -0.011523049  0.005713995 -0.01690565 -0.01147218
## Shape.RollA -0.01474608 -0.006244567  0.016112361 -0.01437808 -0.03050546
## Shape.RollB  0.03115303  0.003914186  0.018056120  0.05224418 -0.03347487
##                        6           7           8          9           10
## Shape.HelTA  0.005090466  0.19951833  0.03704965  1.1185930  0.247941564
## Shape.HelTB -0.056190152 -0.13866218 -0.79277628 -0.2199191 -1.398823776
## Shape.MGW   -0.240438777  0.52234975 -0.84004729  2.2668589 -5.038874279
## Shape.ProT   0.073254740 -0.03301843  0.07058180 -0.1584428 -0.217584887
## Shape.RollA  0.087178350  0.10821079  0.30455687  0.2961529  1.219047333
## Shape.RollB -0.022974180 -0.35985061 -0.31347246 -0.5853085 -0.001892533
##                      11           12          13           14
## Shape.HelTA  0.62344341 -0.394970253  0.43847019  0.085064795
## Shape.HelTB  0.16834722 -0.075493940 -0.04196481 -0.158268536
## Shape.MGW   -1.64321902 -1.028292667  0.85205266 -0.289687871
## Shape.ProT   0.03117504  0.351938000 -0.20401193 -0.004356195
## Shape.RollA  0.17418087  0.003219396 -0.06327993  0.084935775
## Shape.RollB -0.03223779  0.360866595  0.01539779  0.022682681
##                        15          16          17           18
## Shape.HelTA  0.2320359797 -0.06681206  0.06958505  0.031630348
## Shape.HelTB  0.0007406717 -0.14749249 -0.08952829 -0.010917036
## Shape.MGW   -0.0632837504 -0.13965147 -0.03494520 -0.038833639
## Shape.ProT   0.0666495423 -0.02634690 -0.00471992 -0.008383138
## Shape.RollA  0.0729418983  0.07019404  0.05549064  0.025630748
## Shape.RollB -0.0369455267 -0.04667352 -0.03304405  0.003970542
##                       19           20
## Shape.HelTA -0.026124453  0.006796602
## Shape.HelTB -0.030277475  0.005454380
## Shape.MGW   -0.216539493 -0.247302353
## Shape.ProT  -0.001790404  0.025244096
## Shape.RollA  0.013938090  0.076260299
## Shape.RollB -0.059978526 -0.001637988
## 
## Shape beta errors:
##                        1            2            3            4
## Shape.HelTA 0.0010029602 0.0018835861 0.0018322918 0.0017090819
## Shape.HelTB 0.0020717375 0.0020262358 0.0017618077 0.0024013184
## Shape.MGW   0.0043731163 0.0047569197 0.0043433118 0.0051688551
## Shape.ProT  0.0005546923 0.0005448872 0.0005293191 0.0005402752
## Shape.RollA 0.0006356840 0.0012911971 0.0011548558 0.0011613209
## Shape.RollB 0.0013832564 0.0011910830 0.0011377000 0.0011541473
##                        5           6           7           8           9
## Shape.HelTA 0.0025240422 0.002451817 0.004096440 0.009999256 0.027077546
## Shape.HelTB 0.0024642051 0.003112521 0.006357348 0.020247098 0.023913948
## Shape.MGW   0.0055517036 0.005238817 0.010232061 0.030393866 0.047219032
## Shape.ProT  0.0009044745 0.001644376 0.001709128 0.006764151 0.008590887
## Shape.RollA 0.0011143730 0.001802375 0.001473141 0.004240784 0.011531111
## Shape.RollB 0.0016807244 0.001363501 0.003987032 0.010215619 0.012870598
##                     10          11          12          13           14
## Shape.HelTA 0.01815958 0.024223038 0.014617437 0.009811968 0.0033215784
## Shape.HelTB 0.03076439 0.016517651 0.013891849 0.003126885 0.0026158492
## Shape.MGW   0.07322808 0.056539895 0.033439843 0.012511749 0.0053200850
## Shape.ProT  0.01041129 0.010921237 0.007469787 0.002080238 0.0009336091
## Shape.RollA 0.01336729 0.012078431 0.007604200 0.003880516 0.0012600787
## Shape.RollB 0.01153752 0.006690823 0.006477170 0.001430223 0.0010006114
##                      15          16           17           18           19
## Shape.HelTA 0.002499653 0.002328747 0.0018723912 0.0018003705 0.0021455995
## Shape.HelTB 0.002298592 0.001883326 0.0016804326 0.0019580347 0.0020059375
## Shape.MGW   0.005416707 0.004978804 0.0048391228 0.0045536087 0.0050376415
## Shape.ProT  0.000635878 0.000532491 0.0005241211 0.0005410123 0.0005701089
## Shape.RollA 0.001077063 0.001332866 0.0010759384 0.0011305271 0.0013081234
## Shape.RollB 0.001360584 0.001095523 0.0011509634 0.0012506237 0.0014151689
##                       20
## Shape.HelTA 0.0021572144
## Shape.HelTB 0.0011480803
## Shape.MGW   0.0048202040
## Shape.ProT  0.0005785309
## Shape.RollA 0.0015023555
## Shape.RollB 0.0007453678
## 
## [1] "Number of Observations in Design Matrix: 746448"
## No nucleotides included in fit.
## [1] "Stability Reached after 10 iterations."
ModelTest <- finalizeFeatureBetas(ModelTest)

pM <- plot(ModelTest, plotTitle = "HM-Ubx4a-Exd R2 Shape+Fixed Nucleotide Fit", Nplot.ddG = TRUE, verticalPlots = TRUE)
ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.pdf", sep = ""), height = vPheight, width = 6)

save(ModelTest, file = paste(selexDir, saveDir, "/model.RData",sep = ""))
saveRDS(ModelTest, file = paste(selexDir, saveDir, "/model.rds",sep = ""))

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