Multi-round Mononucleotide+Binding View Factor Example (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/MultiroundViewNoSymmetry"
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)
dataSample.R3 = selex.sample(seqName = 'Ubx4a.R3', sampleName = 'HM.Ubx4a.Exd', round = 3)
# 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 = ""))
#data.probeCounts.R3 = getProbeCounts(dataSample.R3, markovModel = mm)
#save(data.probeCounts.R3, file = paste(selexDir, saveDir, "/data.probeCounts.R3.RData", sep = ""))
load(file = paste(selexDir, saveDir, "/data.probeCounts.R3.RData", sep = ""))
# Inputs about library are data specific 
ModelTest = model(name = "HM-Exd-Ubx4a R2+R3 Nucleotide+View Model",
                varRegLen = libLen,
                leftFixedSeq =  "GTTCAGAGTTCTACAGTCCGACGATCTGG", 
                rightFixedSeq ="CCAGCTGTCGTATGCCGTCTTCTGCTTG", 
                consensusSeq = "NTGAYNNAYNNN",
                affinityType = "AffinitySym",
                leftFixedSeqOverlap = 5,
                minAffinity = 0.00,
                missingValueSuppression = 1,
                minSeedValue = .001, 
                upFootprintExtend = 4,
                confidenceLevel = .95, 
                verbose = FALSE,
                includeView = TRUE,
                rounds = list(c(2, 3)),
                rcSymmetric = FALSE)

getFeatureDesign(ModelTest)
## Feature design for object of class 'model'
## 
## seedLen:  12 
## upFootprintExtend:  4 
## downFootprintExtend:  4 
## rcSymmetric:  FALSE 
## 
## Slot "N": 
## N.upFootprintExtend:  4 
## N.downFootprintExtend:  4 
## N.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 
## 
## Slot "Intercept": 
## Number of Views per Strand of DNA: 7
## Number of Rounds: 2 (2, 3)
## Number of previous iterations: 0
## 
## Slot "Shape": 
## "ShapeParamsUsed": NONE
# Add seed model
addSeedPsam(ModelTest) = seedTable2psam(ModelTest, data.kmerTable)

# Model nucleotide Betas after seed PSAM is added
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 Nucleotide Features\nSeeding Model", ddG = TRUE)

Next we score the probes using topModelMatch

sample1 = sample(nrow(data.probeCounts), 500000)
sample2 = sample(nrow(data.probeCounts.R3), 500000)
data = rbind(data.probeCounts[sample1, ], data.probeCounts.R3[sample2, ])
#data = rbind(data.probeCounts, data.probeCounts.R3)
data = topModelMatch(data, ModelTest)
# Uses aligned probes to build design matrix
data = addDesignMatrix(data, ModelTest)
designMatrixSummary = getDesignMatrix(ModelTest, data)
## No shape parameters included in fit.
print("Round summary: ")
## [1] "Round summary: "
print (designMatrixSummary$Round)
##            2      3  Total
## Round 396284 464043 860327
print("Mono-nucleotide summary: ")
## [1] "Mono-nucleotide summary: "
print (designMatrixSummary$N)
##       N.A    N.C    N.G    N.T
## 1   75303 199379 332562 253083
## 2  109946 175452 336129 238800
## 3  153464  94100 401668 211095
## 4  164665 116090 406338 173234
## 5  370377  63320 282297 144333
## 6  104511  21627  19190 714999
## 7  177696   2185 608672  71774
## 8  817398  12314  16679  13936
## 9   42899  16378  42334 758716
## 10  39590   9642  12197 798898
## 11  58694  13383  57188 731062
## 12 836097   5741  13463   5026
## 13  12880 102279  15953 729215
## 14 104507  47681 432467 275672
## 15 371615  49351 302786 136575
## 16 104648 397108 170263 188308
## 17 134348 442408 107660 175911
## 18 256198 349279  98772 156078
## 19 206586 315633 214651 123457
## 20 229288 388252 168154  74633
print("View/strand orientation summary: ")
## [1] "View/strand orientation summary: "
print (designMatrixSummary$Intercept)
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  53715  87778  80056  74296  74994  75920  89450      536209
## Strand.R  38823  54817  50716  39719  41092  43955  54996      324118
# # Constructs regression expression with independent features using design matrix
regressionFormula = updatedRegressionFormula(data, ModelTest)
print("Regression Formula: ")
## [1] "Regression Formula: "
print (regressionFormula)
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.R7"
fit = glm(regressionFormula, 
          data=data, 
          family = poisson(link="log"))
## Warning: glm.fit: fitted rates numerically 0 occurred
summary(fit)
## 
## Call:
## glm(formula = regressionFormula, family = poisson(link = "log"), 
##     data = data)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -14.9398   -0.9594   -0.3371    0.2471   19.3409  
## 
## Coefficients:
##               Estimate Std. Error  z value Pr(>|z|)    
## (Intercept) 25.9799985  0.0068299 3803.887  < 2e-16 ***
## Round.2     -0.8665432  0.0026337 -329.019  < 2e-16 ***
## N.A1         0.0217454  0.0012258   17.740  < 2e-16 ***
## N.C1        -0.0302969  0.0013662  -22.175  < 2e-16 ***
## N.T1        -0.0472560  0.0012461  -37.923  < 2e-16 ***
## N.A2         0.0410221  0.0010229   40.103  < 2e-16 ***
## N.C2        -0.0321541  0.0011539  -27.865  < 2e-16 ***
## N.T2        -0.0543052  0.0010612  -51.175  < 2e-16 ***
## N.A3         0.0498994  0.0008729   57.165  < 2e-16 ***
## N.C3        -0.0968250  0.0010588  -91.448  < 2e-16 ***
## N.T3        -0.0704332  0.0009303  -75.713  < 2e-16 ***
## N.A4         0.0100403  0.0007863   12.769  < 2e-16 ***
## N.C4        -0.1536739  0.0009697 -158.481  < 2e-16 ***
## N.T4        -0.0712809  0.0007985  -89.263  < 2e-16 ***
## N.C5        -0.7904000  0.0016125 -490.159  < 2e-16 ***
## N.G5        -0.2773901  0.0006816 -406.942  < 2e-16 ***
## N.T5        -0.4214655  0.0007485 -563.044  < 2e-16 ***
## N.A6        -0.8704441  0.0014585 -596.807  < 2e-16 ***
## N.C6        -1.6016940  0.0079441 -201.622  < 2e-16 ***
## N.G6        -1.8827779  0.0122596 -153.576  < 2e-16 ***
## N.A7        -0.6417588  0.0008219 -780.829  < 2e-16 ***
## N.C7        -2.5228323  0.0801031  -31.495  < 2e-16 ***
## N.T7        -1.1216813  0.0018218 -615.707  < 2e-16 ***
## N.C8        -2.1071077  0.0214821  -98.087  < 2e-16 ***
## N.G8        -2.0512367  0.0160076 -128.142  < 2e-16 ***
## N.T8        -2.1593982  0.0170036 -126.997  < 2e-16 ***
## N.A9        -1.2859220  0.0036356 -353.707  < 2e-16 ***
## N.C9        -1.7866818  0.0123163 -145.067  < 2e-16 ***
## N.G9        -1.2735565  0.0035905 -354.700  < 2e-16 ***
## N.A10       -1.4238814  0.0042499 -335.037  < 2e-16 ***
## N.C10       -2.0531408  0.0243104  -84.455  < 2e-16 ***
## N.G10       -1.9329191  0.0203386  -95.037  < 2e-16 ***
## N.A11       -1.0232666  0.0020661 -495.262  < 2e-16 ***
## N.C11       -1.3729521  0.0095626 -143.575  < 2e-16 ***
## N.G11       -0.9769796  0.0021602 -452.271  < 2e-16 ***
## N.C12       -2.3444628  0.0464466  -50.477  < 2e-16 ***
## N.G12       -2.0743761  0.0181614 -114.219  < 2e-16 ***
## N.T12       -2.4283005  0.0421698  -57.584  < 2e-16 ***
## N.A13       -1.8788434  0.0133411 -140.831  < 2e-16 ***
## N.C13       -0.5632526  0.0011216 -502.184  < 2e-16 ***
## N.G13       -1.6668076  0.0099424 -167.646  < 2e-16 ***
## N.A14       -0.6263215  0.0011135 -562.484  < 2e-16 ***
## N.C14       -0.7800215  0.0017887 -436.090  < 2e-16 ***
## N.T14       -0.1496742  0.0005430 -275.622  < 2e-16 ***
## N.C15       -0.8978080  0.0021493 -417.725  < 2e-16 ***
## N.G15       -0.1185204  0.0005634 -210.368  < 2e-16 ***
## N.T15       -0.5144171  0.0008750 -587.872  < 2e-16 ***
## N.A16       -0.4563735  0.0009957 -458.327  < 2e-16 ***
## N.G16       -0.2177338  0.0007484 -290.917  < 2e-16 ***
## N.T16       -0.2602191  0.0007143 -364.304  < 2e-16 ***
## N.A17       -0.1793964  0.0008792 -204.046  < 2e-16 ***
## N.G17       -0.2460541  0.0009929 -247.818  < 2e-16 ***
## N.T17       -0.0779527  0.0007804  -99.887  < 2e-16 ***
## N.A18       -0.0838812  0.0010672  -78.596  < 2e-16 ***
## N.G18       -0.0881562  0.0011178  -78.865  < 2e-16 ***
## N.T18        0.0715949  0.0009332   76.719  < 2e-16 ***
## N.A19       -0.0620947  0.0012296  -50.498  < 2e-16 ***
## N.G19       -0.1066724  0.0013405  -79.579  < 2e-16 ***
## N.T19        0.1011834  0.0010821   93.504  < 2e-16 ***
## N.A20       -0.0318163  0.0015224  -20.899  < 2e-16 ***
## N.G20       -0.0715558  0.0016216  -44.126  < 2e-16 ***
## N.T20        0.0687244  0.0013848   49.627  < 2e-16 ***
## Strand.F1   -0.0712535  0.0025283  -28.182  < 2e-16 ***
## Strand.R1   -0.0006337  0.0028143   -0.225    0.822    
## Strand.F2    0.1354451  0.0023313   58.098  < 2e-16 ***
## Strand.R2    0.1202413  0.0024733   48.615  < 2e-16 ***
## Strand.F3    0.0815021  0.0019924   40.906  < 2e-16 ***
## Strand.R3    0.0835060  0.0022255   37.522  < 2e-16 ***
## Strand.F4    0.0266087  0.0021866   12.169  < 2e-16 ***
## Strand.R4    0.0102616  0.0024421    4.202 2.65e-05 ***
## Strand.F5    0.0611707  0.0026997   22.658  < 2e-16 ***
## Strand.R5    0.0432092  0.0029039   14.880  < 2e-16 ***
## Strand.F6    0.0569660  0.0025979   21.928  < 2e-16 ***
## Strand.R6    0.0869046  0.0027671   31.407  < 2e-16 ***
## Strand.R7    0.0141537  0.0020409    6.935 4.07e-12 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for poisson family taken to be 1)
## 
##     Null deviance: 6057390  on 860326  degrees of freedom
## Residual deviance: 1445731  on 860252  degrees of freedom
## AIC: 2643025
## 
## Number of Fisher Scoring iterations: 9
ModelTest = addNewBetas(ModelTest, data, fit)
## No shape parameters included in fit.
# # Nucleotide Features after first round of fitting
summary(ModelTest)
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3           4          5          6
## N.A  0.02174536  0.04102213  0.04989937  0.01004026  0.0000000 -0.8704441
## N.C -0.03029691 -0.03215409 -0.09682500 -0.15367389 -0.7904000 -1.6016940
## N.G  0.00000000  0.00000000  0.00000000  0.00000000 -0.2773901 -1.8827779
## N.T -0.04725599 -0.05430520 -0.07043318 -0.07128095 -0.4214655  0.0000000
##              7         8         9        10         11        12
## N.A -0.6417588  0.000000 -1.285922 -1.423881 -1.0232666  0.000000
## N.C -2.5228323 -2.107108 -1.786682 -2.053141 -1.3729521 -2.344463
## N.G  0.0000000 -2.051237 -1.273557 -1.932919 -0.9769796 -2.074376
## N.T -1.1216813 -2.159398  0.000000  0.000000  0.0000000 -2.428301
##             13         14         15         16          17          18
## N.A -1.8788434 -0.6263215  0.0000000 -0.4563735 -0.17939643 -0.08388117
## N.C -0.5632526 -0.7800215 -0.8978080  0.0000000  0.00000000  0.00000000
## N.G -1.6668076  0.0000000 -0.1185204 -0.2177338 -0.24605412 -0.08815617
## N.T  0.0000000 -0.1496742 -0.5144171 -0.2602191 -0.07795266  0.07159492
##              19          20
## N.A -0.06209466 -0.03181629
## N.C  0.00000000  0.00000000
## N.G -0.10667238 -0.07155580
## N.T  0.10118344  0.06872438
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001225789 0.001022926 0.0008728981 0.0007863284 0.0000000000
## N.C 0.001366243 0.001153924 0.0010587979 0.0009696662 0.0016125376
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006816458
## N.T 0.001246089 0.001061175 0.0009302660 0.0007985459 0.0007485479
##               6            7          8           9          10
## N.A 0.001458502 0.0008218937 0.00000000 0.003635556 0.004249926
## N.C 0.007944050 0.0801030965 0.02148208 0.012316281 0.024310364
## N.G 0.012259566 0.0000000000 0.01600757 0.003590522 0.020338560
## N.T 0.000000000 0.0018217765 0.01700359 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002066110 0.00000000 0.013341077 0.0011134916 0.0000000000
## N.C 0.009562609 0.04644656 0.001121606 0.0017886722 0.0021492824
## N.G 0.002160162 0.01816142 0.009942423 0.0000000000 0.0005633947
## N.T 0.000000000 0.04216979 0.000000000 0.0005430418 0.0008750489
##               16           17          18          19          20
## N.A 0.0009957372 0.0008791966 0.001067247 0.001229638 0.001522355
## N.C 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## N.G 0.0007484384 0.0009928808 0.001117817 0.001340463 0.001621621
## N.T 0.0007142913 0.0007804081 0.000933205 0.001082135 0.001384808
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1  View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.04220 25.2489 25.19496 25.14006 25.17463 25.17042 25.11346
## Strand.R 25.11282 25.2337 25.19696 25.12372 25.15666 25.20036 25.12761
## 
## Round.3:
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7
## Strand.F  25.98  25.98  25.98  25.98  25.98  25.98  25.98
## Strand.R  25.98  25.98  25.98  25.98  25.98  25.98  25.98
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.007744408 0.007682350 0.007586380 0.007639668 0.007802040
## Strand.R 0.007842412 0.007726627 0.007650909 0.007716672 0.007875033
##               View.6      View.7
## Strand.F 0.007767393 0.007320068
## Strand.R 0.007825608 0.007599266
## 
## Round.3:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.006829856 0.006829856 0.006829856 0.006829856 0.006829856
## Strand.R 0.006829856 0.006829856 0.006829856 0.006829856 0.006829856
##               View.6      View.7
## Strand.F 0.006829856 0.006829856
## Strand.R 0.006829856 0.006829856
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
vPheight = verticalPlot_height(ModelTest)
pM <- plot(ModelTest, plotTitle = "HM-Ubx4a-Exd R2+R3 Nucleotide+View 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)

some text

data = rbind(data.probeCounts[sample1, ], data.probeCounts.R3[sample2, ])
#data = rbind(data.probeCounts, data.probeCounts.R3)
data.nrow = nrow(data)
data = topModelMatch(data, ModelTest)
data = addDesignMatrix(data, ModelTest)
designMatrixSummary.v2 = getDesignMatrix(ModelTest, data)
## No shape parameters included in fit.
if ((all(designMatrixSummary.v2$N == designMatrixSummary$N)) & (all(designMatrixSummary.v2$Round == designMatrixSummary$Round)) & (all(designMatrixSummary.v2$Intercept == designMatrixSummary$Intercept)))  {
  print ("Stability Reached")
}
for (i in 2:20) {
  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$Intercept)
  # # Constructs regression expression with independent features using design matrix
  regressionFormula = updatedRegressionFormula(data, ModelTest)
  print("Regression Formula: ")
  print (regressionFormula)
  fit = glm(regressionFormula, 
            data=data, 
            family = poisson(link="log"))
  summary(fit)
  ModelTest = addNewBetas(ModelTest, data, fit)
  # # Nucleotide Features after first round of fitting
  summary(ModelTest)
  pM <- plot(ModelTest, plotTitle = "HM-Ubx4a-Exd R2+R3 Nucleotide+View Fit", Nplot.ddG = TRUE, verticalPlots = TRUE)
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.pdf", sep = ""), height = vPheight, width = 6)
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.",i, ".pdf", sep = ""), height = vPheight, width = 6)
  data = topModelMatch(data, ModelTest)
  data = addDesignMatrix(data, ModelTest)
  designMatrixSummary.v2 = getDesignMatrix(ModelTest, data)
  print(paste("Number of Observations in Design Matrix: ",nrow(data), sep = ""))
  if ((all(designMatrixSummary.v2$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 if (nrow(data) == 0) {
    print ("Algorithm failed to converge: No probes meet the confidence level requirement (Confidence Level:", ModelTest@confidenceLevel, ")", sep = "")
  }
}
## [1] "i = 2"
## No shape parameters included in fit.
## [1] "Round summary: "
##            2      3  Total
## Round 375596 459331 834927
## [1] "Mono-nucleotide summary: "
##       N.A    N.C    N.G    N.T
## 1   71839 194863 322264 245961
## 2  106756 169446 327801 230924
## 3  148348  91555 391477 203547
## 4  161174 110479 395291 167983
## 5  363332  61164 270955 139476
## 6   96191  20341  15977 702418
## 7  170122   1945 593862  68998
## 8  796895  11065  13694  13273
## 9   34242  13198  36699 750788
## 10  33151   7834  10323 783619
## 11  50985  12686  54761 716495
## 12 811450   6367  11490   5620
## 13   9558 105889  12521 706959
## 14 102714  46854 427685 257674
## 15 355809  49806 291172 138140
## 16 101462 383910 169598 179957
## 17 130452 429056 104062 171357
## 18 246481 338823  95758 153865
## 19 199773 307234 206459 121461
## 20 221683 377768 162748  72728
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  51928  86099  78478  72935  72746  73536  85642      521364
## Strand.R  37574  53366  49645  38581  39636  42252  52509      313563
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3            4          5          6
## N.A  0.02161680  0.04116163  0.04968048  0.009676129  0.0000000 -0.8703624
## N.C -0.03080325 -0.03190743 -0.09711335 -0.153391713 -0.7902572 -1.6002163
## N.G  0.00000000  0.00000000  0.00000000  0.000000000 -0.2769111 -1.9038633
## N.T -0.04743797 -0.05350019 -0.07058902 -0.071120573 -0.4209625  0.0000000
##              7         8         9        10         11        12
## N.A -0.6418182  0.000000 -1.276362 -1.422949 -1.0157410  0.000000
## N.C -2.5258672 -2.120071 -1.789571 -2.075350 -1.3637884 -2.334191
## N.G  0.0000000 -2.096095 -1.275476 -1.952938 -0.9779989 -2.096544
## N.T -1.1222207 -2.155269  0.000000  0.000000  0.0000000 -2.465743
##            13         14         15         16          17          18
## N.A -1.893950 -0.6256484  0.0000000 -0.4558603 -0.17955429 -0.08374309
## N.C -0.563107 -0.7809584 -0.8975121  0.0000000  0.00000000  0.00000000
## N.G -1.668017  0.0000000 -0.1188200 -0.2177312 -0.24587791 -0.08831218
## N.T  0.000000 -0.1491573 -0.5138728 -0.2599798 -0.07778824  0.07166771
##              19          20
## N.A -0.06183125 -0.03186788
## N.C  0.00000000  0.00000000
## N.G -0.10639641 -0.07169170
## N.T  0.10134188  0.06853919
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001227401 0.001023550 0.0008735877 0.0007863359 0.0000000000
## N.C 0.001367158 0.001155034 0.0010591287 0.0009715764 0.0016132155
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006823636
## N.T 0.001247362 0.001062273 0.0009307194 0.0007985833 0.0007490592
##               6            7          8           9          10
## N.A 0.001461079 0.0008209909 0.00000000 0.003809889 0.004359196
## N.C 0.007908856 0.0826646719 0.02180765 0.012518961 0.025197804
## N.G 0.012712334 0.0000000000 0.01713440 0.003613790 0.021276997
## N.T 0.000000000 0.0018219500 0.01688406 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002089993 0.00000000 0.013747033 0.0011130465 0.0000000000
## N.C 0.009457113 0.04518970 0.001116826 0.0017851658 0.0021446679
## N.G 0.002164481 0.01871764 0.010022616 0.0000000000 0.0005638808
## N.T 0.000000000 0.04289796 0.000000000 0.0005437652 0.0008734697
##               16           17          18          19          20
## N.A 0.0009958352 0.0008795767 0.001067556 0.001230283 0.001523163
## N.C 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## N.G 0.0007480090 0.0009933159 0.001118673 0.001341109 0.001622679
## N.T 0.0007151687 0.0007804032 0.000933293 0.001082684 0.001385523
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.17768 25.38413 25.33084 25.27575 25.31053 25.30653 25.24928
## Strand.R 25.24831 25.36903 25.33300 25.25965 25.29231 25.33610 25.26348
## 
## Round.3:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 26.38251 26.38251 26.38251 26.38251 26.38251 26.38251 26.38251
## Strand.R 26.38251 26.38251 26.38251 26.38251 26.38251 26.38251 26.38251
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.008330157 0.007963591 0.008284461 0.008349883 0.008324490
## Strand.R 0.008437961 0.008084675 0.008353475 0.008436064 0.008409874
##               View.6      View.7
## Strand.F 0.008290195 0.008298123
## Strand.R 0.008351975 0.008346303
## 
## Round.3:
##              View.1     View.2     View.3     View.4     View.5     View.6
## Strand.F 0.00745047 0.00745047 0.00745047 0.00745047 0.00745047 0.00745047
## Strand.R 0.00745047 0.00745047 0.00745047 0.00745047 0.00745047 0.00745047
##              View.7
## Strand.F 0.00745047
## Strand.R 0.00745047
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
## No shape parameters included in fit.
## [1] "Number of Observations in Design Matrix: 833942"
## [1] "i = 3"
## No shape parameters included in fit.
## [1] "Round summary: "
##            2      3  Total
## Round 374969 458973 833942
## [1] "Mono-nucleotide summary: "
##       N.A    N.C    N.G    N.T
## 1   71718 194705 321779 245740
## 2  106604 169268 327387 230683
## 3  148168  91377 391162 203235
## 4  160925 110258 394985 167774
## 5  362808  61110 270658 139366
## 6   96109  20314  15856 701663
## 7  169711   1926 593499  68806
## 8  796204  11028  13457  13253
## 9   34220  13154  36641 749927
## 10  33111   7795  10247 782789
## 11  50943  12658  54703 715638
## 12 810668   6365  11407   5502
## 13   9493 105801  12490 706158
## 14 102584  46753 427342 257263
## 15 355341  49738 290922 137941
## 16 101297 383491 169442 179712
## 17 130310 428514 103957 171161
## 18 246225 338334  95670 153713
## 19 199513 306825 206241 121363
## 20 221405 377351 162523  72663
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  51873  86018  78419  72819  72611  73419  85527      520686
## Strand.R  37550  53343  49618  38518  39585  42183  52459      313256
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3            4          5          6
## N.A  0.02161796  0.04118556  0.04967212  0.009706826  0.0000000 -0.8703717
## N.C -0.03078716 -0.03188387 -0.09707026 -0.153371718 -0.7902692 -1.6003049
## N.G  0.00000000  0.00000000  0.00000000  0.000000000 -0.2769103 -1.9035372
## N.T -0.04744382 -0.05349705 -0.07060092 -0.071126095 -0.4209607  0.0000000
##              7         8         9        10         11        12
## N.A -0.6417425  0.000000 -1.276403 -1.422914 -1.0157639  0.000000
## N.C -2.5580154 -2.121431 -1.789558 -2.073904 -1.3633777 -2.334184
## N.G  0.0000000 -2.099540 -1.275492 -1.952250 -0.9780047 -2.097386
## N.T -1.1222256 -2.155701  0.000000  0.000000  0.0000000 -2.459204
##             13         14         15         16          17          18
## N.A -1.8946767 -0.6256303  0.0000000 -0.4558612 -0.17954685 -0.08371906
## N.C -0.5631081 -0.7808180 -0.8974941  0.0000000  0.00000000  0.00000000
## N.G -1.6678461  0.0000000 -0.1188129 -0.2177189 -0.24585769 -0.08829377
## N.T  0.0000000 -0.1491417 -0.5138710 -0.2599724 -0.07777757  0.07168990
##              19          20
## N.A -0.06183264 -0.03187252
## N.C  0.00000000  0.00000000
## N.G -0.10639138 -0.07169272
## N.T  0.10133614  0.06853261
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001227526 0.001023691 0.0008736130 0.0007863773 0.0000000000
## N.C 0.001367240 0.001155174 0.0010592226 0.0009717609 0.0016132812
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006824038
## N.T 0.001247467 0.001062414 0.0009308357 0.0007986143 0.0007490782
##               6            7          8           9          10
## N.A 0.001461145 0.0008213274 0.00000000 0.003810101 0.004359167
## N.C 0.007912005 0.0861170085 0.02184313 0.012526982 0.025191209
## N.G 0.012720213 0.0000000000 0.01725742 0.003614000 0.021294860
## N.T 0.000000000 0.0018224720 0.01689473 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002090092 0.00000000 0.013772455 0.0011131499 0.0000000000
## N.C 0.009461385 0.04518967 0.001116882 0.0017852495 0.0021448480
## N.G 0.002164582 0.01874735 0.010022326 0.0000000000 0.0005639128
## N.T 0.000000000 0.04286689 0.000000000 0.0005437987 0.0008735590
##               16           17           18          19          20
## N.A 0.0009959992 0.0008796166 0.0010676227 0.001230316 0.001523172
## N.C 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## N.G 0.0007480350 0.0009933683 0.0011187333 0.001341108 0.001622686
## N.T 0.0007152181 0.0007804453 0.0009333569 0.001082688 0.001385530
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.17758 25.38401 25.33073 25.27564 25.31044 25.30643 25.24917
## Strand.R 25.24820 25.36891 25.33289 25.25954 25.29223 25.33597 25.26338
## 
## Round.3:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231
## Strand.R 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.008330632 0.007964043 0.008284932 0.008350361 0.008324955
## Strand.R 0.008438430 0.008085123 0.008353942 0.008436572 0.008410352
##               View.6      View.7
## Strand.F 0.008290659 0.008298572
## Strand.R 0.008352454 0.008346759
## 
## Round.3:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.007450878 0.007450878 0.007450878 0.007450878 0.007450878
## Strand.R 0.007450878 0.007450878 0.007450878 0.007450878 0.007450878
##               View.6      View.7
## Strand.F 0.007450878 0.007450878
## Strand.R 0.007450878 0.007450878
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
## No shape parameters included in fit.
## [1] "Number of Observations in Design Matrix: 833892"
## [1] "i = 4"
## No shape parameters included in fit.
## [1] "Round summary: "
##            2      3  Total
## Round 374939 458953 833892
## [1] "Mono-nucleotide summary: "
##       N.A    N.C    N.G    N.T
## 1   71711 194700 321757 245724
## 2  106594 169264 327359 230675
## 3  148155  91370 391146 203221
## 4  160915 110253 394966 167758
## 5  362783  61109 270644 139356
## 6   96098  20313  15852 701629
## 7  169705   1895 593488  68804
## 8  796171  11023  13447  13251
## 9   34214  13153  36634 749891
## 10  33108   7794  10246 782744
## 11  50937  12658  54698 715599
## 12 810623   6365  11402   5502
## 13   9493 105795  12487 706117
## 14 102578  46749 427316 257249
## 15 355324  49732 290903 137933
## 16 101292 383463 169434 179703
## 17 130302 428484 103953 171153
## 18 246205 338316  95664 153707
## 19 199505 306802 206226 121359
## 20 221393 377322 162516  72661
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  51871  86016  78416  72813  72605  73416  85516      520653
## Strand.R  37550  53342  49614  38514  39583  42181  52455      313239
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3            4          5          6
## N.A  0.02161878  0.04117861  0.04967106  0.009710873  0.0000000 -0.8703706
## N.C -0.03078533 -0.03188463 -0.09706984 -0.153367766 -0.7902677 -1.6003030
## N.G  0.00000000  0.00000000  0.00000000  0.000000000 -0.2769090 -1.9035339
## N.T -0.04744182 -0.05350018 -0.07060485 -0.071122836 -0.4209594  0.0000000
##              7         8         9        10         11        12
## N.A -0.6417498  0.000000 -1.276432 -1.422912 -1.0157506  0.000000
## N.C -2.5768151 -2.121421 -1.789558 -2.073903 -1.3633770 -2.334183
## N.G  0.0000000 -2.099419 -1.275491 -1.952249 -0.9780042 -2.097381
## N.T -1.1222202 -2.155700  0.000000  0.000000  0.0000000 -2.459204
##             13         14         15         16          17          18
## N.A -1.8946760 -0.6256280  0.0000000 -0.4558732 -0.17954842 -0.08371902
## N.C -0.5631074 -0.7808113 -0.8974931  0.0000000  0.00000000  0.00000000
## N.G -1.6678462  0.0000000 -0.1188133 -0.2177190 -0.24585968 -0.08829375
## N.T  0.0000000 -0.1491395 -0.5138794 -0.2599719 -0.07778302  0.07168998
##              19          20
## N.A -0.06183268 -0.03187245
## N.C  0.00000000  0.00000000
## N.G -0.10639137 -0.07169273
## N.T  0.10133631  0.06853280
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001227530 0.001023696 0.0008736138 0.0007863803 0.0000000000
## N.C 0.001367242 0.001155174 0.0010592224 0.0009717629 0.0016132808
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006824041
## N.T 0.001247469 0.001062416 0.0009308394 0.0007986175 0.0007490784
##               6            7          8           9          10
## N.A 0.001461144 0.0008213357 0.00000000 0.003810345 0.004359166
## N.C 0.007912002 0.0883528511 0.02184309 0.012526978 0.025191202
## N.G 0.012720207 0.0000000000 0.01725711 0.003613999 0.021294855
## N.T 0.000000000 0.0018224688 0.01689473 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002090083 0.00000000 0.013772451 0.0011131499 0.0000000000
## N.C 0.009461380 0.04518965 0.001116881 0.0017852463 0.0021448475
## N.G 0.002164582 0.01874736 0.010022322 0.0000000000 0.0005639128
## N.T 0.000000000 0.04286688 0.000000000 0.0005437994 0.0008735694
##               16           17           18          19          20
## N.A 0.0009960150 0.0008796163 0.0010676224 0.001230315 0.001523171
## N.C 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## N.G 0.0007480348 0.0009933679 0.0011187330 0.001341108 0.001622686
## N.T 0.0007152178 0.0007804473 0.0009333566 0.001082687 0.001385529
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.17759 25.38401 25.33073 25.27565 25.31045 25.30643 25.24918
## Strand.R 25.24821 25.36892 25.33289 25.25954 25.29221 25.33597 25.26338
## 
## Round.3:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233
## Strand.R 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.008330637 0.007964048 0.008284937 0.008350367 0.008324960
## Strand.R 0.008438435 0.008085128 0.008353947 0.008436578 0.008410366
##               View.6      View.7
## Strand.F 0.008290664 0.008298577
## Strand.R 0.008352459 0.008346764
## 
## Round.3:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.007450883 0.007450883 0.007450883 0.007450883 0.007450883
## Strand.R 0.007450883 0.007450883 0.007450883 0.007450883 0.007450883
##               View.6      View.7
## Strand.F 0.007450883 0.007450883
## Strand.R 0.007450883 0.007450883
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
## No shape parameters included in fit.
## [1] "Number of Observations in Design Matrix: 833864"
## [1] "i = 5"
## No shape parameters included in fit.
## [1] "Round summary: "
##            2      3  Total
## Round 374925 458939 833864
## [1] "Mono-nucleotide summary: "
##       N.A    N.C    N.G    N.T
## 1   71711 194695 321746 245712
## 2  106592 169257 327349 230666
## 3  148149  91369 391131 203215
## 4  160914 110251 394951 167748
## 5  362774  61108 270633 139349
## 6   96093  20312  15851 701608
## 7  169705   1867 593488  68804
## 8  796146  11021  13447  13250
## 9   34208  13151  36633 749872
## 10  33108   7793  10245 782718
## 11  50937  12657  54695 715575
## 12 810600   6365  11398   5501
## 13   9492 105791  12483 706098
## 14 102573  46749 427301 257241
## 15 355316  49729 290889 137930
## 16 101286 383450 169429 179699
## 17 130296 428470 103952 171146
## 18 246197 338303  95662 153702
## 19 199499 306790 206223 121352
## 20 221383 377311 162513  72657
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  51866  86013  78415  72810  72600  73413  85515      520632
## Strand.R  37549  53340  49610  38514  39583  42181  52455      313232
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3            4          5          6
## N.A  0.02161999  0.04117954  0.04967045  0.009710779  0.0000000 -0.8703704
## N.C -0.03078413 -0.03188370 -0.09706996 -0.153367846 -0.7902675 -1.6003027
## N.G  0.00000000  0.00000000  0.00000000  0.000000000 -0.2769088 -1.9035337
## N.T -0.04744057 -0.05349907 -0.07060494 -0.071123369 -0.4209592  0.0000000
##              7         8         9        10         11        12
## N.A -0.6417498  0.000000 -1.276431 -1.422912 -1.0157504  0.000000
## N.C -2.5870079 -2.121420 -1.789557 -2.073903 -1.3633767 -2.334182
## N.G  0.0000000 -2.099419 -1.275491 -1.952248 -0.9780041 -2.097380
## N.T -1.1222200 -2.155699  0.000000  0.000000  0.0000000 -2.459204
##             13         14         15         16          17          18
## N.A -1.8946757 -0.6256278  0.0000000 -0.4558727 -0.17954837 -0.08371896
## N.C -0.5631072 -0.7808110 -0.8974931  0.0000000  0.00000000  0.00000000
## N.G -1.6678459  0.0000000 -0.1188135 -0.2177187 -0.24585970 -0.08829378
## N.T  0.0000000 -0.1491393 -0.5138793 -0.2599715 -0.07778303  0.07169001
##              19          20
## N.A -0.06183269 -0.03187242
## N.C  0.00000000  0.00000000
## N.G -0.10639136 -0.07169273
## N.T  0.10133642  0.06853291
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001227531 0.001023697 0.0008736141 0.0007863802 0.0000000000
## N.C 0.001367243 0.001155175 0.0010592223 0.0009717629 0.0016132807
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006824041
## N.T 0.001247470 0.001062416 0.0009308394 0.0007986178 0.0007490784
##               6            7          8           9          10
## N.A 0.001461144 0.0008213357 0.00000000 0.003810345 0.004359165
## N.C 0.007912002 0.0899421774 0.02184309 0.012526976 0.025191201
## N.G 0.012720206 0.0000000000 0.01725711 0.003613999 0.021294854
## N.T 0.000000000 0.0018224687 0.01689473 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002090083 0.00000000 0.013772451 0.0011131499 0.0000000000
## N.C 0.009461380 0.04518965 0.001116881 0.0017852463 0.0021448474
## N.G 0.002164582 0.01874735 0.010022322 0.0000000000 0.0005639130
## N.T 0.000000000 0.04286688 0.000000000 0.0005437995 0.0008735694
##               16           17           18          19          20
## N.A 0.0009960150 0.0008796162 0.0010676224 0.001230315 0.001523171
## N.C 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## N.G 0.0007480349 0.0009933678 0.0011187330 0.001341108 0.001622686
## N.T 0.0007152179 0.0007804473 0.0009333566 0.001082687 0.001385529
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.17758 25.38401 25.33073 25.27565 25.31045 25.30642 25.24917
## Strand.R 25.24820 25.36891 25.33289 25.25954 25.29221 25.33597 25.26337
## 
## Round.3:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 26.38232 26.38232 26.38232 26.38232 26.38232 26.38232 26.38232
## Strand.R 26.38232 26.38232 26.38232 26.38232 26.38232 26.38232 26.38232
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2     View.3      View.4      View.5
## Strand.F 0.008330640 0.007964051 0.00828494 0.008350370 0.008324964
## Strand.R 0.008438438 0.008085131 0.00835395 0.008436581 0.008410370
##               View.6      View.7
## Strand.F 0.008290667 0.008298580
## Strand.R 0.008352462 0.008346768
## 
## Round.3:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.007450886 0.007450886 0.007450886 0.007450886 0.007450886
## Strand.R 0.007450886 0.007450886 0.007450886 0.007450886 0.007450886
##               View.6      View.7
## Strand.F 0.007450886 0.007450886
## Strand.R 0.007450886 0.007450886
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
## No shape parameters included in fit.
## [1] "Number of Observations in Design Matrix: 833852"
## [1] "i = 6"
## No shape parameters included in fit.
## [1] "Round summary: "
##            2      3  Total
## Round 374921 458931 833852
## [1] "Mono-nucleotide summary: "
##       N.A    N.C    N.G    N.T
## 1   71709 194693 321741 245709
## 2  106589 169255 327345 230663
## 3  148146  91368 391127 203211
## 4  160911 110250 394947 167744
## 5  362770  61108 270627 139347
## 6   96092  20312  15851 701597
## 7  169705   1855 593488  68804
## 8  796135  11021  13447  13249
## 9   34208  13151  36632 749861
## 10  33108   7793  10245 782706
## 11  50935  12656  54694 715567
## 12 810589   6364  11398   5501
## 13   9491 105788  12483 706090
## 14 102572  46749 427295 257236
## 15 355311  49729 290884 137928
## 16 101284 383443 169427 179698
## 17 130293 428463 103951 171145
## 18 246191 338300  95662 153699
## 19 199498 306785 206217 121352
## 20 221378 377306 162511  72657
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  51865  86012  78415  72810  72598  73412  85513      520625
## Strand.R  37549  53340  49610  38512  39583  42181  52452      313227
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3            4          5          6
## N.A  0.02161825  0.04117977  0.04966963  0.009709965  0.0000000 -0.8703704
## N.C -0.03078405 -0.03188357 -0.09706995 -0.153367863 -0.7902674 -1.6003029
## N.G  0.00000000  0.00000000  0.00000000  0.000000000 -0.2769086 -1.9035342
## N.T -0.04744063 -0.05350064 -0.07060499 -0.071123372 -0.4209590  0.0000000
##              7         8         9        10         11        12
## N.A -0.6417498  0.000000 -1.276431 -1.422912 -1.0157504  0.000000
## N.C -2.6097849 -2.121420 -1.789557 -2.073903 -1.3633767 -2.334183
## N.G  0.0000000 -2.099419 -1.275491 -1.952249 -0.9780041 -2.097380
## N.T -1.1222204 -2.155699  0.000000  0.000000  0.0000000 -2.459204
##             13         14         15         16          17          18
## N.A -1.8946757 -0.6256280  0.0000000 -0.4558727 -0.17954842 -0.08371897
## N.C -0.5631071 -0.7808113 -0.8974934  0.0000000  0.00000000  0.00000000
## N.G -1.6678460  0.0000000 -0.1188141 -0.2177187 -0.24585972 -0.08829387
## N.T  0.0000000 -0.1491400 -0.5138796 -0.2599716 -0.07778299  0.07169009
##              19          20
## N.A -0.06183273 -0.03187236
## N.C  0.00000000  0.00000000
## N.G -0.10639137 -0.07169273
## N.T  0.10133660  0.06853307
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001227533 0.001023697 0.0008736147 0.0007863807 0.0000000000
## N.C 0.001367243 0.001155175 0.0010592224 0.0009717629 0.0016132808
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006824042
## N.T 0.001247471 0.001062418 0.0009308394 0.0007986178 0.0007490785
##               6            7          8           9          10
## N.A 0.001461145 0.0008213358 0.00000000 0.003810345 0.004359166
## N.C 0.007912002 0.0925527845 0.02184309 0.012526977 0.025191202
## N.G 0.012720207 0.0000000000 0.01725711 0.003613999 0.021294855
## N.T 0.000000000 0.0018224689 0.01689473 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002090083 0.00000000 0.013772452 0.0011131500 0.0000000000
## N.C 0.009461380 0.04518965 0.001116881 0.0017852465 0.0021448476
## N.G 0.002164582 0.01874735 0.010022323 0.0000000000 0.0005639132
## N.T 0.000000000 0.04286688 0.000000000 0.0005437997 0.0008735694
##               16           17           18          19          20
## N.A 0.0009960150 0.0008796162 0.0010676224 0.001230315 0.001523171
## N.C 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## N.G 0.0007480349 0.0009933678 0.0011187330 0.001341108 0.001622686
## N.T 0.0007152179 0.0007804473 0.0009333565 0.001082687 0.001385529
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.17758 25.38401 25.33073 25.27565 25.31045 25.30643 25.24918
## Strand.R 25.24820 25.36892 25.33289 25.25955 25.29221 25.33597 25.26338
## 
## Round.3:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233
## Strand.R 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233 26.38233
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.008330642 0.007964053 0.008284942 0.008350372 0.008324965
## Strand.R 0.008438440 0.008085132 0.008353952 0.008436583 0.008410371
##               View.6      View.7
## Strand.F 0.008290669 0.008298582
## Strand.R 0.008352464 0.008346770
## 
## Round.3:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.007450887 0.007450887 0.007450887 0.007450887 0.007450887
## Strand.R 0.007450887 0.007450887 0.007450887 0.007450887 0.007450887
##               View.6      View.7
## Strand.F 0.007450887 0.007450887
## Strand.R 0.007450887 0.007450887
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
## No shape parameters included in fit.
## [1] "Number of Observations in Design Matrix: 833824"
## [1] "i = 7"
## No shape parameters included in fit.
## [1] "Round summary: "
##            2      3  Total
## Round 374910 458914 833824
## [1] "Mono-nucleotide summary: "
##       N.A    N.C    N.G    N.T
## 1   71706 194686 321727 245705
## 2  106586 169248 327335 230655
## 3  148138  91364 391117 203205
## 4  160909 110246 394930 167739
## 5  362755  61106 270617 139346
## 6   96083  20310  15849 701582
## 7  169705   1827 593488  68804
## 8  796110  11021  13447  13246
## 9   34208  13149  36630 749837
## 10  33108   7793  10245 782678
## 11  50933  12656  54686 715549
## 12 810565   6364  11395   5500
## 13   9490 105781  12481 706072
## 14 102570  46746 427279 257229
## 15 355307  49726 290868 137923
## 16 101278 383435 169419 179692
## 17 130286 428451 103949 171138
## 18 246183 338288  95658 153695
## 19 199489 306772 206214 121349
## 20 221370 377295 162505  72654
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  51863  86007  78415  72805  72596  73408  85512      520606
## Strand.R  37547  53339  49609  38511  39581  42180  52451      313218
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3            4          5          6
## N.A  0.02161840  0.04117965  0.04966979  0.009709798  0.0000000 -0.8703708
## N.C -0.03078414 -0.03188381 -0.09707008 -0.153368116 -0.7902676 -1.6004906
## N.G  0.00000000  0.00000000  0.00000000  0.000000000 -0.2769084 -1.9035352
## N.T -0.04744066 -0.05350078 -0.07060502 -0.071123473 -0.4209590  0.0000000
##              7        8         9        10         11        12
## N.A -0.6417501  0.00000 -1.276431 -1.422913 -1.0157509  0.000000
## N.C -2.6318832 -2.12142 -1.789557 -2.073904 -1.3633770 -2.334183
## N.G  0.0000000 -2.09942 -1.275492 -1.952249 -0.9780044 -2.097380
## N.T -1.1222210 -2.15570  0.000000  0.000000  0.0000000 -2.459205
##             13         14         15         16          17          18
## N.A -1.8946764 -0.6256285  0.0000000 -0.4558724 -0.17954756 -0.08371728
## N.C -0.5631074 -0.7808119 -0.8974942  0.0000000  0.00000000  0.00000000
## N.G -1.6678466  0.0000000 -0.1188147 -0.2177183 -0.24585878 -0.08829211
## N.T  0.0000000 -0.1491407 -0.5138800 -0.2599711 -0.07778197  0.07169193
##              19          20
## N.A -0.06183278 -0.03186858
## N.C  0.00000000  0.00000000
## N.G -0.10639140 -0.07168890
## N.T  0.10133573  0.06853711
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001227533 0.001023697 0.0008736147 0.0007863807 0.0000000000
## N.C 0.001367243 0.001155175 0.0010592224 0.0009717630 0.0016132810
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006824043
## N.T 0.001247471 0.001062418 0.0009308394 0.0007986178 0.0007490786
##               6            7          8           9          10
## N.A 0.001461145 0.0008213359 0.00000000 0.003810345 0.004359167
## N.C 0.007913761 0.0953633815 0.02184309 0.012526979 0.025191206
## N.G 0.012720209 0.0000000000 0.01725711 0.003614000 0.021294857
## N.T 0.000000000 0.0018224692 0.01689473 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002090083 0.00000000 0.013772454 0.0011131501 0.0000000000
## N.C 0.009461381 0.04518965 0.001116882 0.0017852467 0.0021448479
## N.G 0.002164582 0.01874735 0.010022325 0.0000000000 0.0005639135
## N.T 0.000000000 0.04286689 0.000000000 0.0005437999 0.0008735695
##               16           17           18          19          20
## N.A 0.0009960152 0.0008796167 0.0010676236 0.001230315 0.001523176
## N.C 0.0000000000 0.0000000000 0.0000000000 0.000000000 0.000000000
## N.G 0.0007480351 0.0009933682 0.0011187341 0.001341108 0.001622689
## N.T 0.0007152181 0.0007804478 0.0009333579 0.001082688 0.001385534
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.17758 25.38401 25.33073 25.27565 25.31045 25.30642 25.24917
## Strand.R 25.24820 25.36891 25.33289 25.25954 25.29220 25.33597 25.26337
## 
## Round.3:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231
## Strand.R 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.008330653 0.007964064 0.008284954 0.008350384 0.008324976
## Strand.R 0.008438451 0.008085144 0.008353964 0.008436594 0.008410382
##               View.6      View.7
## Strand.F 0.008290680 0.008298593
## Strand.R 0.008352475 0.008346781
## 
## Round.3:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.007450898 0.007450898 0.007450898 0.007450898 0.007450898
## Strand.R 0.007450898 0.007450898 0.007450898 0.007450898 0.007450898
##               View.6      View.7
## Strand.F 0.007450898 0.007450898
## Strand.R 0.007450898 0.007450898
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
## No shape parameters included in fit.
## [1] "Number of Observations in Design Matrix: 833789"
## [1] "i = 8"
## No shape parameters included in fit.
## [1] "Round summary: "
##            2      3  Total
## Round 374895 458894 833789
## [1] "Mono-nucleotide summary: "
##       N.A    N.C    N.G    N.T
## 1   71700 194679 321717 245693
## 2  106582 169242 327321 230644
## 3  148132  91359 391100 203198
## 4  160901 110242 394914 167732
## 5  362740  61105 270608 139336
## 6   96076  20309  15847 701557
## 7  169704   1793 593488  68804
## 8  796079  11019  13447  13244
## 9   34207  13147  36625 749810
## 10  33108   7792  10243 782646
## 11  50931  12655  54680 715523
## 12 810531   6364  11394   5500
## 13   9490 105773  12481 706045
## 14 102565  46745 427261 257218
## 15 355292  49725 290854 137918
## 16 101273 383420 169410 179686
## 17 130282 428434 103941 171132
## 18 246172 338274  95656 153687
## 19 199482 306760 206207 121340
## 20 221362 377278 162499  72650
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 StrandTotal
## Strand.F  51861  86003  78412  72802  72593  73405  85509      520585
## Strand.R  37546  53337  49604  38509  39580  42179  52449      313204
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+Round.2+N.A1+N.C1+N.T1+N.A2+N.C2+N.T2+N.A3+N.C3+N.T3+N.A4+N.C4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.A7+N.C7+N.T7+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.A10+N.C10+N.G10+N.A11+N.C11+N.G11+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.A14+N.C14+N.T14+N.C15+N.G15+N.T15+N.A16+N.G16+N.T16+N.A17+N.G17+N.T17+N.A18+N.G18+N.T18+N.A19+N.G19+N.T19+N.A20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  HM-Exd-Ubx4a R2+R3 Nucleotide+View 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":  0.001 
## 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 features  with 7 view(s) per strand of DNA and 2 round(s) of data (round = 2, 3) without reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.2+Round.3+N.A1+N.C1+N.G1+N.T1+N.A2+N.C2+N.G2+N.T2+N.A3+N.C3+N.G3+N.T3+N.A4+N.C4+N.G4+N.T4+N.A5+N.C5+N.G5+N.T5+N.A6+N.C6+N.G6+N.T6+N.A7+N.C7+N.G7+N.T7+N.A8+N.C8+N.G8+N.T8+N.A9+N.C9+N.G9+N.T9+N.A10+N.C10+N.G10+N.T10+N.A11+N.C11+N.G11+N.T11+N.A12+N.C12+N.G12+N.T12+N.A13+N.C13+N.G13+N.T13+N.A14+N.C14+N.G14+N.T14+N.A15+N.C15+N.G15+N.T15+N.A16+N.C16+N.G16+N.T16+N.A17+N.C17+N.G17+N.T17+N.A18+N.C18+N.G18+N.T18+N.A19+N.C19+N.G19+N.T19+N.A20+N.C20+N.G20+N.T20+Strand.F1+Strand.R1+Strand.F2+Strand.R2+Strand.F3+Strand.R3+Strand.F4+Strand.R4+Strand.F5+Strand.R5+Strand.F6+Strand.R6+Strand.F7+Strand.R7 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 20 nucleotides for a feature model of length 20.
## Nucleotide beta values:
##               1           2           3            4          5          6
## N.A  0.02161860  0.04117961  0.04967003  0.009709794  0.0000000 -0.8703707
## N.C -0.03078417 -0.03188383 -0.09707003 -0.153368139 -0.7902676 -1.6004530
## N.G  0.00000000  0.00000000  0.00000000  0.000000000 -0.2769084 -1.9035350
## N.T -0.04744019 -0.05350029 -0.07060498 -0.071123275 -0.4209590  0.0000000
##              7         8         9        10         11        12
## N.A -0.6417497  0.000000 -1.276431 -1.422913 -1.0157509  0.000000
## N.C -2.6252853 -2.121421 -1.789557 -2.073904 -1.3633771 -2.334183
## N.G  0.0000000 -2.099420 -1.275492 -1.952249 -0.9780044 -2.097381
## N.T -1.1222210 -2.155700  0.000000  0.000000  0.0000000 -2.459205
##             13         14         15         16          17          18
## N.A -1.8946765 -0.6256284  0.0000000 -0.4558724 -0.17954758 -0.08371732
## N.C -0.5631074 -0.7808118 -0.8974941  0.0000000  0.00000000  0.00000000
## N.G -1.6678467  0.0000000 -0.1188147 -0.2177183 -0.24585878 -0.08829214
## N.T  0.0000000 -0.1491405 -0.5138800 -0.2599711 -0.07778201  0.07169187
##              19          20
## N.A -0.06183277 -0.03186843
## N.C  0.00000000  0.00000000
## N.G -0.10639139 -0.07168888
## N.T  0.10133575  0.06853708
## 
## Nucleotide beta errors:
##               1           2            3            4            5
## N.A 0.001227533 0.001023697 0.0008736146 0.0007863807 0.0000000000
## N.C 0.001367243 0.001155175 0.0010592224 0.0009717630 0.0016132810
## N.G 0.000000000 0.000000000 0.0000000000 0.0000000000 0.0006824043
## N.T 0.001247470 0.001062418 0.0009308395 0.0007986177 0.0007490786
##               6            7          8           9          10
## N.A 0.001461145 0.0008213358 0.00000000 0.003810345 0.004359167
## N.C 0.007913704 0.0954336610 0.02184309 0.012526979 0.025191206
## N.G 0.012720209 0.0000000000 0.01725711 0.003614000 0.021294858
## N.T 0.000000000 0.0018224692 0.01689473 0.000000000 0.000000000
##              11         12          13           14           15
## N.A 0.002090083 0.00000000 0.013772454 0.0011131501 0.0000000000
## N.C 0.009461382 0.04518965 0.001116882 0.0017852467 0.0021448479
## N.G 0.002164582 0.01874736 0.010022325 0.0000000000 0.0005639135
## N.T 0.000000000 0.04286689 0.000000000 0.0005437999 0.0008735695
##               16           17          18          19          20
## N.A 0.0009960152 0.0008796168 0.001067624 0.001230315 0.001523176
## N.C 0.0000000000 0.0000000000 0.000000000 0.000000000 0.000000000
## N.G 0.0007480352 0.0009933682 0.001118734 0.001341108 0.001622689
## N.T 0.0007152181 0.0007804478 0.000933358 0.001082688 0.001385534
## 
## 
## An object of class 'Intercept'
## Fits 14 views and 2 round(s) (round = 2, 3).
## Intercept beta values:
## Round.2:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 25.17758 25.38401 25.33073 25.27565 25.31044 25.30642 25.24917
## Strand.R 25.24820 25.36891 25.33289 25.25954 25.29220 25.33596 25.26337
## 
## Round.3:
##            View.1   View.2   View.3   View.4   View.5   View.6   View.7
## Strand.F 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231
## Strand.R 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231 26.38231
## 
## Intercept beta errors:
## Round.2:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.008330653 0.007964064 0.008284954 0.008350384 0.008324977
## Strand.R 0.008438451 0.008085144 0.008353964 0.008436595 0.008410383
##               View.6      View.7
## Strand.F 0.008290680 0.008298594
## Strand.R 0.008352475 0.008346781
## 
## Round.3:
##               View.1      View.2      View.3      View.4      View.5
## Strand.F 0.007450899 0.007450899 0.007450899 0.007450899 0.007450899
## Strand.R 0.007450899 0.007450899 0.007450899 0.007450899 0.007450899
##               View.6      View.7
## Strand.F 0.007450899 0.007450899
## Strand.R 0.007450899 0.007450899
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 20.
## No shape parameters included in fit.
## [1] "Number of Observations in Design Matrix: 833789"
## [1] "Stability Reached after 8 iterations."
ModelTest <- finalizeFeatureBetas(ModelTest)

pM <- plot(ModelTest, plotTitle = "HM-Ubx4a-Exd R2+R3 Nucleotide+View 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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