Mononucleotide + Binding View Factor Reverse Complement-Symmetric Example

Gabriella Martini

2016-07-11

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/Pufall/"
processedDataDir = "/Users/gabriella/Columbia/SplitFastqData/Pufall/ConcatFiles/"
# CLUSTER VERSIONS ARE COMMENTED OUT
#selexDir = "/vega/hblab/users/gdm2120/SELEX/SELEX/"
#rawdataDir = "/vega/hblab/projects/selex/rawdata/Pufall"
#processedDataDir = "/vega/hblab/users/gdm2120/SplitFastqData/Pufall/"
##################################################################

saveDir = "gabriella/SelexGLMtest/ViewSymmetry"
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.Pufall',
                   paste(processedDataDir, "/Demultiplexed.R0.fastq.gz", sep = ""),
                   'r0',
                   0, 23, '', 'TGGAA')


selex.defineSample('AR.R8',
                   paste(processedDataDir,"/AR.R8.fastq.gz",sep = ""),
                   'AR-DBD',
                   8, 23, '', 'TGGAA')


selex.defineSample('AR.R7',
                   paste(processedDataDir,"/AR.R7.fastq.gz",sep = ""),
                   'AR-DBD',
                   7, 23, '', 'TGGAA')





r0 = selex.sample(seqName = 'r0.Pufall', sampleName='r0', round = 0)
r0.split = selex.split(r0)
r0.train = r0.split$train
r0.test = r0.split$test
dataSample = selex.sample(seqName = 'AR.R8', sampleName = 'AR-DBD', round = 8)
# MARKOV MODEL BUILT
kmax = selex.kmax(sample = r0.test)
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))
kLen = 15



#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 = ""))
# Inputs about library are data specific 
ModelTest = model(name = "AR-DBD R8 Nucleotides+View (Rev. Comp. Sym.)",
                varRegLen = libLen,
                leftFixedSeq =  "GTTCAGAGTTCTACAGTCCGACGATC",
                rightFixedSeq ="TGGAATTCTCGGGTGCCAAGG", 
                consensusSeq = "RGWACANNNTGTWCY",
                affinityType = "AffinitySym",
                leftFixedSeqOverlap = 5,
                minAffinity = 0.01,
                missingValueSuppression = .5,
                minSeedValue = .01, 
                upFootprintExtend = 4,
                confidenceLevel = .99, 
                rounds = list(c(8)),
                rcSymmetric = TRUE,
                verbose = FALSE,
                includeView = TRUE)

getFeatureDesign(ModelTest)
## Feature design for object of class 'model'
## 
## seedLen:  15 
## upFootprintExtend:  4 
## downFootprintExtend:  4 
## rcSymmetric:  TRUE 
## 
## 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 21 22 23 
## Number of previous iterations:  0 
## 
## Slot "Intercept": 
## Number of Views per Strand of DNA: 11
## Number of Rounds: 1 (8)
## 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
## N.A 0 0 0 0  0.00000000 -1.2968295 -0.03073087  0.000000 -1.296829
## N.C 0 0 0 0 -0.60728754 -1.2968295 -0.25628921 -1.296829  0.000000
## N.G 0 0 0 0 -0.09864725  0.0000000 -0.34036727 -1.296829 -1.296829
## N.T 0 0 0 0 -0.42644057 -0.5591611  0.00000000 -1.296829 -1.296829
##             10          11         12          13         14        15
## N.A  0.0000000 -0.40799975 -0.1359377 -0.09020211 -0.7968295 -1.296829
## N.C -1.2968295  0.00000000  0.0000000 -0.36546623 -0.3957275 -1.296829
## N.G -0.3957275 -0.36546623  0.0000000  0.00000000 -1.2968295  0.000000
## N.T -0.7968295 -0.09020211 -0.1359377 -0.40799975  0.0000000 -1.296829
##            16          17         18          19 20 21 22 23
## N.A -1.296829  0.00000000 -0.5591611 -0.42644057  0  0  0  0
## N.C -1.296829 -0.34036727  0.0000000 -0.09864725  0  0  0  0
## N.G -1.296829 -0.25628921 -1.2968295 -0.60728754  0  0  0  0
## N.T  0.000000 -0.03073087 -1.2968295  0.00000000  0  0  0  0
plot(ModelTest@features@N, Ntitle = "AR-DBD R8 Nucleotides+View\nSeeding 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)
designMatrixSummary = getDesignMatrix(ModelTest, data)
## No shape parameters included in fit.
print("Round summary: ")
## [1] "Round summary: "
print (designMatrixSummary$Round)
##            8  Total
## Round 999419 999419
print("View/strand orientation summary: ")
## [1] "View/strand orientation summary: "
print (designMatrixSummary$Intercept)
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 View.8 View.9
## Strand.F   5114  64609  97214  69970 107435 129518 141254 154187 111083
## Strand.R      0      0      0      0      0      0      0      0      0
##          View.10 View.11 StrandTotal
## Strand.F   56898   62137      999419
## Strand.R       0       0           0
print("Mono-nucleotide summary: ")
## [1] "Mono-nucleotide summary: "
print (designMatrixSummary$N)
##        N.A     N.C     N.G    N.T
## 1   583106  638621  349297 427814
## 2   719215  470626  372502 436495
## 3   909957  500103  170875 417903
## 4   928055  254670  407530 408583
## 5  1290774   18245  647452  42367
## 6      628     235 1982654  15321
## 7   843239  104864   93707 957028
## 8  1996427     416    1112    883
## 9      567 1997333     351    587
## 10 1880160     651  115054   2973
## 11   80236 1114706  111699 692197
## 12  343341  656078       0      0
# # 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)+N.A1+N.G1+N.T1+N.C2+N.G2+N.T2+N.C3+N.G3+N.T3+N.C4+N.G4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.T6+N.A7+N.C7+N.G7+N.C8+N.G8+N.T8+N.A9+N.G9+N.T9+N.C10+N.G10+N.T10+N.A11+N.G11+N.T11+N.A12+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F9+Strand.F10+Strand.F11"
fit = glm(regressionFormula, 
          data=data, 
          family = poisson(link="log"))
summary(fit)
## 
## Call:
## glm(formula = regressionFormula, family = poisson(link = "log"), 
##     data = data)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -20.438   -1.466   -0.740    0.255   49.993  
## 
## Coefficients:
##               Estimate Std. Error   z value Pr(>|z|)    
## (Intercept) 36.7310541  0.0025161 14598.186  < 2e-16 ***
## N.A1        -0.0007886  0.0001885    -4.183 2.88e-05 ***
## N.G1        -0.0013041  0.0001963    -6.643 3.06e-11 ***
## N.T1        -0.0406328  0.0002126  -191.130  < 2e-16 ***
## N.C2        -0.0839757  0.0001967  -426.826  < 2e-16 ***
## N.G2        -0.0201035  0.0001506  -133.452  < 2e-16 ***
## N.T2        -0.0907762  0.0001875  -484.017  < 2e-16 ***
## N.C3        -0.1167444  0.0001886  -618.915  < 2e-16 ***
## N.G3        -0.1663480  0.0002364  -703.674  < 2e-16 ***
## N.T3        -0.1281815  0.0001696  -755.994  < 2e-16 ***
## N.C4        -0.1851119  0.0003186  -581.098  < 2e-16 ***
## N.G4        -0.0858129  0.0001570  -546.607  < 2e-16 ***
## N.T4        -0.1089580  0.0001546  -704.882  < 2e-16 ***
## N.C5        -0.3165167  0.0012400  -255.264  < 2e-16 ***
## N.G5        -0.0836743  0.0001311  -638.204  < 2e-16 ***
## N.T5        -0.2948046  0.0006279  -469.511  < 2e-16 ***
## N.A6        -0.6970147  0.0255158   -27.317  < 2e-16 ***
## N.C6        -0.7379696  0.0472457   -15.620  < 2e-16 ***
## N.T6        -0.3319334  0.0011583  -286.568  < 2e-16 ***
## N.A7         0.0043403  0.0001105    39.269  < 2e-16 ***
## N.C7        -0.1653976  0.0002938  -562.984  < 2e-16 ***
## N.G7        -0.2073225  0.0003989  -519.716  < 2e-16 ***
## N.C8        -0.8847915  0.0721689   -12.260  < 2e-16 ***
## N.G8        -0.6641571  0.0164138   -40.463  < 2e-16 ***
## N.T8        -0.7708278  0.0232124   -33.208  < 2e-16 ***
## N.A9        -0.9143806  0.0625001   -14.630  < 2e-16 ***
## N.G9        -0.9011112  0.0721689   -12.486  < 2e-16 ***
## N.T9        -0.7379939  0.0272505   -27.082  < 2e-16 ***
## N.C10       -0.7201365  0.0286772   -25.112  < 2e-16 ***
## N.G10       -0.2182459  0.0003182  -685.848  < 2e-16 ***
## N.T10       -0.5641030  0.0049090  -114.911  < 2e-16 ***
## N.A11       -0.2781574  0.0004215  -659.994  < 2e-16 ***
## N.G11       -0.2139864  0.0003267  -654.936  < 2e-16 ***
## N.T11       -0.0677985  0.0001205  -562.585  < 2e-16 ***
## N.A12       -0.1076231  0.0001778  -605.444  < 2e-16 ***
## Strand.F1   -0.0663117  0.0022999   -28.833  < 2e-16 ***
## Strand.F2    0.0349913  0.0005637    62.070  < 2e-16 ***
## Strand.F3    0.0494918  0.0004394   112.643  < 2e-16 ***
## Strand.F4    0.0099097  0.0004535    21.849  < 2e-16 ***
## Strand.F5   -0.0043029  0.0002740   -15.702  < 2e-16 ***
## Strand.F6    0.0242601  0.0002834    85.594  < 2e-16 ***
## Strand.F7    0.0184938  0.0003140    58.894  < 2e-16 ***
## Strand.F9   -0.0527175  0.0003470  -151.943  < 2e-16 ***
## Strand.F10  -0.0320581  0.0005529   -57.984  < 2e-16 ***
## Strand.F11   0.0659849  0.0006508   101.385  < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for poisson family taken to be 1)
## 
##     Null deviance: 9127258  on 999418  degrees of freedom
## Residual deviance: 4719719  on 999374  degrees of freedom
## AIC: 6158726
## 
## Number of Fisher Scoring iterations: 10
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":  AR-DBD R8 Nucleotides+View (Rev. Comp. Sym.) 
## Slot "varRegLen":  23 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATC 
## Slot "rightFixedSeq":  TGGAATTCTCGGGTGCCAAGG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.99 
## Slot "minAffinity":  0.01 
## Slot "missingValueSuppression":  0.5 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  15 
## Slot "consensusSeq":  [AG]G[AT]ACA[ACGT][ACGT][ACGT]TGT[AT]C[CT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  23 
## 
## Fits a model of footprint length 23 for mono-nucleotide features with 11 view(s) per strand of DNA and 1 round(s) of data (round = 8) with reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.8+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+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F8+Strand.F9+Strand.F10+Strand.F11 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 23 nucleotides for a feature model of length 23.
## Nucleotide features are reverse complement symmetric.
## Nucleotide beta values:
##                 1           2          3           4           5
## N.A -0.0007886279  0.00000000  0.0000000  0.00000000  0.00000000
## N.C  0.0000000000 -0.08397569 -0.1167444 -0.18511185 -0.31651670
## N.G -0.0013040805 -0.02010354 -0.1663480 -0.08581288 -0.08367433
## N.T -0.0406328207 -0.09077622 -0.1281815 -0.10895800 -0.29480465
##              6           7          8          9         10          11
## N.A -0.6970147  0.00434026  0.0000000 -0.9143806  0.0000000 -0.27815739
## N.C -0.7379696 -0.16539761 -0.8847915  0.0000000 -0.7201365  0.00000000
## N.G  0.0000000 -0.20732247 -0.6641571 -0.9011112 -0.2182459 -0.21398638
## N.T -0.3319334  0.00000000 -0.7708278 -0.7379939 -0.5641030 -0.06779855
##             12          13         14         15         16          17
## N.A -0.1076231 -0.06779855 -0.5641030 -0.7379939 -0.7708278  0.00000000
## N.C  0.0000000 -0.21398638 -0.2182459 -0.9011112 -0.6641571 -0.20732247
## N.G  0.0000000  0.00000000 -0.7201365  0.0000000 -0.8847915 -0.16539761
## N.T -0.1076231 -0.27815739  0.0000000 -0.9143806  0.0000000  0.00434026
##             18          19          20         21          22
## N.A -0.3319334 -0.29480465 -0.10895800 -0.1281815 -0.09077622
## N.C  0.0000000 -0.08367433 -0.08581288 -0.1663480 -0.02010354
## N.G -0.7379696 -0.31651670 -0.18511185 -0.1167444 -0.08397569
## N.T -0.6970147  0.00000000  0.00000000  0.0000000  0.00000000
##                23
## N.A -0.0406328207
## N.C -0.0013040805
## N.G  0.0000000000
## N.T -0.0007886279
## 
## Nucleotide beta errors:
##                1            2            3            4            5
## N.A 0.0001885477 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## N.C 0.0000000000 0.0001967447 0.0001886277 0.0003185556 0.0012399564
## N.G 0.0001962952 0.0001506426 0.0002363993 0.0001569920 0.0001311092
## N.T 0.0002125931 0.0001875475 0.0001695536 0.0001545762 0.0006278971
##               6            7          8          9           10
## N.A 0.025515796 0.0001105268 0.00000000 0.06250013 0.0000000000
## N.C 0.047245671 0.0002937873 0.07216888 0.00000000 0.0286772225
## N.G 0.000000000 0.0003989147 0.01641375 0.07216894 0.0003182131
## N.T 0.001158308 0.0000000000 0.02321237 0.02725052 0.0049090436
##               11           12           13           14         15
## N.A 0.0004214543 0.0001777591 0.0001205125 0.0049090436 0.02725052
## N.C 0.0000000000 0.0000000000 0.0003267288 0.0003182131 0.07216894
## N.G 0.0003267288 0.0000000000 0.0000000000 0.0286772225 0.00000000
## N.T 0.0001205125 0.0001777591 0.0004214543 0.0000000000 0.06250013
##             16           17          18           19           20
## N.A 0.02321237 0.0000000000 0.001158308 0.0006278971 0.0001545762
## N.C 0.01641375 0.0003989147 0.000000000 0.0001311092 0.0001569920
## N.G 0.07216888 0.0002937873 0.047245671 0.0012399564 0.0003185556
## N.T 0.00000000 0.0001105268 0.025515796 0.0000000000 0.0000000000
##               21           22           23
## N.A 0.0001695536 0.0001875475 0.0002125931
## N.C 0.0002363993 0.0001506426 0.0001962952
## N.G 0.0001886277 0.0001967447 0.0000000000
## N.T 0.0000000000 0.0000000000 0.0001885477
## 
## 
## An object of class 'Intercept'
## Fits 11 views and 1 round(s) (round = 8).
## Intercept beta values:
## Round.8:
##              View.1   View.2   View.3   View.4   View.5   View.6   View.7
## StrandView 36.66474 36.76605 36.78055 36.74096 36.72675 36.75531 36.74955
##              View.8   View.9 View.10  View.11
## StrandView 36.73105 36.67834  36.699 36.79704
## 
## Intercept beta errors:
## Round.8:
##                 View.1      View.2      View.3      View.4      View.5
## StrandView 0.003408863 0.002578517 0.002554211 0.002556689 0.002531017
##                 View.6      View.7      View.8      View.9     View.10
## StrandView 0.002532052 0.002535658 0.002516138 0.002539947 0.002576165
##                View.11
## StrandView 0.002598949
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 23.
vPheight = verticalPlot_height(ModelTest)
pM <- plot(ModelTest, plotTitle = "AR-DBD R8 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 = data.probeCounts[sample1,]
#data = data.probeCounts
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 shape parameters 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 = designMatrixSummary.v2
  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 = "AR-DBD R8 Nucleotide+View Fit", Nplot.ddG = TRUE, verticalPlots = TRUE)
  
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.",i, ".pdf", sep = ""), height = vPheight, width = 6)
  
  ggplot2::ggsave(pM, file = paste(selexDir, saveDir, "/modelPlot.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"
## [1] "Round summary: "
##            8  Total
## Round 999499 999499
## [1] "Mono-nucleotide summary: "
##        N.A     N.C     N.G    N.T
## 1   583129  638711  349320 427838
## 2   719251  470686  372545 436516
## 3   910027  500144  170882 417945
## 4   928110  254680  407559 408649
## 5  1290827   18295  647486  42390
## 6      655     260 1982705  15378
## 7   843287  104894   93740 957077
## 8  1996497     428    1149    924
## 9      587 1997417     378    616
## 10 1880189     673  115119   3017
## 11   80276 1114759  111735 692228
## 12  343386  656113       0      0
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 View.8 View.9
## Strand.F   5134  64610  97217  69981 107445 129529 141258 154199 111098
## Strand.R      0      0      0      0      0      0      0      0      0
##          View.10 View.11 StrandTotal
## Strand.F   56899   62129      999499
## Strand.R       0       0           0
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+N.A1+N.G1+N.T1+N.C2+N.G2+N.T2+N.C3+N.G3+N.T3+N.C4+N.G4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.T6+N.A7+N.C7+N.G7+N.C8+N.G8+N.T8+N.A9+N.G9+N.T9+N.C10+N.G10+N.T10+N.A11+N.G11+N.T11+N.A12+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F9+Strand.F10+Strand.F11"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  AR-DBD R8 Nucleotides+View (Rev. Comp. Sym.) 
## Slot "varRegLen":  23 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATC 
## Slot "rightFixedSeq":  TGGAATTCTCGGGTGCCAAGG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.99 
## Slot "minAffinity":  0.01 
## Slot "missingValueSuppression":  0.5 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  15 
## Slot "consensusSeq":  [AG]G[AT]ACA[ACGT][ACGT][ACGT]TGT[AT]C[CT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  23 
## 
## Fits a model of footprint length 23 for mono-nucleotide features with 11 view(s) per strand of DNA and 1 round(s) of data (round = 8) with reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.8+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+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F8+Strand.F9+Strand.F10+Strand.F11 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 23 nucleotides for a feature model of length 23.
## Nucleotide features are reverse complement symmetric.
## Nucleotide beta values:
##                 1           2          3           4           5
## N.A -0.0007896198  0.00000000  0.0000000  0.00000000  0.00000000
## N.C  0.0000000000 -0.08396499 -0.1167259 -0.18511354 -0.31652166
## N.G -0.0013046356 -0.02010428 -0.1663337 -0.08579961 -0.08366557
## N.T -0.0406326555 -0.09076936 -0.1281664 -0.10894253 -0.29474760
##              6            7          8          9         10          11
## N.A -0.6969883  0.004345207  0.0000000 -0.7195810  0.0000000 -0.27812246
## N.C -0.5264337 -0.165372011 -0.8488055  0.0000000 -0.6510970  0.00000000
## N.G  0.0000000 -0.207274056 -0.5972905 -0.6264243 -0.2181908 -0.21394646
## N.T -0.3315207  0.000000000 -0.7131216 -0.7643796 -0.5574950 -0.06778797
##             12          13         14         15         16           17
## N.A -0.1076119 -0.06778797 -0.5574950 -0.7643796 -0.7131216  0.000000000
## N.C  0.0000000 -0.21394646 -0.2181908 -0.6264243 -0.5972905 -0.207274056
## N.G  0.0000000  0.00000000 -0.6510970  0.0000000 -0.8488055 -0.165372011
## N.T -0.1076119 -0.27812246  0.0000000 -0.7195810  0.0000000  0.004345207
##             18          19          20         21          22
## N.A -0.3315207 -0.29474760 -0.10894253 -0.1281664 -0.09076936
## N.C  0.0000000 -0.08366557 -0.08579961 -0.1663337 -0.02010428
## N.G -0.5264337 -0.31652166 -0.18511354 -0.1167259 -0.08396499
## N.T -0.6969883  0.00000000  0.00000000  0.0000000  0.00000000
##                23
## N.A -0.0406326555
## N.C -0.0013046356
## N.G  0.0000000000
## N.T -0.0007896198
## 
## Nucleotide beta errors:
##                1            2            3            4            5
## N.A 0.0001885457 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## N.C 0.0000000000 0.0001967431 0.0001886260 0.0003185814 0.0012401360
## N.G 0.0001962929 0.0001506426 0.0002364026 0.0001569925 0.0001311098
## N.T 0.0002125927 0.0001875480 0.0001695537 0.0001545747 0.0006278391
##               6            7          8          9           10
## N.A 0.025515795 0.0001105268 0.00000000 0.02867724 0.0000000000
## N.C 0.020016271 0.0002937798 0.06250011 0.00000000 0.0217600440
## N.G 0.000000000 0.0003988762 0.01256356 0.02404406 0.0003181755
## N.T 0.001156562 0.0000000000 0.01843081 0.03031726 0.0047819218
##               11           12           13           14         15
## N.A 0.0004214381 0.0001777579 0.0001205125 0.0047819218 0.03031726
## N.C 0.0000000000 0.0000000000 0.0003267069 0.0003181755 0.02404406
## N.G 0.0003267069 0.0000000000 0.0000000000 0.0217600440 0.00000000
## N.T 0.0001205125 0.0001777579 0.0004214381 0.0000000000 0.02867724
##             16           17          18           19           20
## N.A 0.01843081 0.0000000000 0.001156562 0.0006278391 0.0001545747
## N.C 0.01256356 0.0003988762 0.000000000 0.0001311098 0.0001569925
## N.G 0.06250011 0.0002937798 0.020016271 0.0012401360 0.0003185814
## N.T 0.00000000 0.0001105268 0.025515795 0.0000000000 0.0000000000
##               21           22           23
## N.A 0.0001695537 0.0001875480 0.0002125927
## N.C 0.0002364026 0.0001506426 0.0001962929
## N.G 0.0001886260 0.0001967431 0.0000000000
## N.T 0.0000000000 0.0000000000 0.0001885457
## 
## 
## An object of class 'Intercept'
## Fits 11 views and 1 round(s) (round = 8).
## Intercept beta values:
## Round.8:
##              View.1   View.2 View.3   View.4   View.5   View.6   View.7
## StrandView 36.66472 36.76554  36.78 36.74043 36.72621 36.75478 36.74901
##              View.8   View.9  View.10  View.11
## StrandView 36.73052 36.67781 36.69849 36.79652
## 
## Intercept beta errors:
## Round.8:
##                 View.1      View.2      View.3      View.4      View.5
## StrandView 0.003406914 0.002578583 0.002554277 0.002556754 0.002531084
##                 View.6      View.7      View.8      View.9     View.10
## StrandView 0.002532118 0.002535724 0.002516205 0.002540013 0.002576221
##                View.11
## StrandView 0.002599016
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 23.
## [1] "Number of Observations in Design Matrix: 999462"
## No shape parameters included in fit.
## [1] "i = 3"
## [1] "Round summary: "
##            8  Total
## Round 999462 999462
## [1] "Mono-nucleotide summary: "
##        N.A     N.C     N.G    N.T
## 1   583114  638677  349311 427822
## 2   719230  470664  372528 436502
## 3   910009  500115  170873 417927
## 4   928090  254655  407544 408635
## 5  1290800   18283  647473  42368
## 6      637     258 1982663  15366
## 7   843266  104882   93727 957049
## 8  1996461     418    1140    905
## 9      579 1997368     378    599
## 10 1880162     667  115096   2999
## 11   80256 1114740  111720 692208
## 12  343364  656098       0      0
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 View.8 View.9
## Strand.F   5129  64607  97216  69977 107444 129527 141257 154188 111094
## Strand.R      0      0      0      0      0      0      0      0      0
##          View.10 View.11 StrandTotal
## Strand.F   56898   62125      999462
## Strand.R       0       0           0
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+N.A1+N.G1+N.T1+N.C2+N.G2+N.T2+N.C3+N.G3+N.T3+N.C4+N.G4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.T6+N.A7+N.C7+N.G7+N.C8+N.G8+N.T8+N.A9+N.G9+N.T9+N.C10+N.G10+N.T10+N.A11+N.G11+N.T11+N.A12+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F9+Strand.F10+Strand.F11"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  AR-DBD R8 Nucleotides+View (Rev. Comp. Sym.) 
## Slot "varRegLen":  23 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATC 
## Slot "rightFixedSeq":  TGGAATTCTCGGGTGCCAAGG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.99 
## Slot "minAffinity":  0.01 
## Slot "missingValueSuppression":  0.5 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  15 
## Slot "consensusSeq":  [AG]G[AT]ACA[ACGT][ACGT][ACGT]TGT[AT]C[CT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  23 
## 
## Fits a model of footprint length 23 for mono-nucleotide features with 11 view(s) per strand of DNA and 1 round(s) of data (round = 8) with reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.8+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+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F8+Strand.F9+Strand.F10+Strand.F11 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 23 nucleotides for a feature model of length 23.
## Nucleotide features are reverse complement symmetric.
## Nucleotide beta values:
##                 1           2          3           4          5          6
## N.A -0.0007890804  0.00000000  0.0000000  0.00000000  0.0000000 -0.7023137
## N.C  0.0000000000 -0.08396657 -0.1167290 -0.18511814 -0.3165396 -0.5264819
## N.G -0.0013038695 -0.02010472 -0.1663383 -0.08580149 -0.0836681  0.0000000
## N.T -0.0406333798 -0.09077066 -0.1281696 -0.10894495 -0.2947557 -0.3315261
##                7          8          9         10          11         12
## N.A  0.004345295  0.0000000 -0.7491354  0.0000000 -0.27813239 -0.1076146
## N.C -0.165379542 -0.8488090  0.0000000 -0.6809039  0.00000000  0.0000000
## N.G -0.207282190 -0.5985633 -0.6264306 -0.2181970 -0.21395878  0.0000000
## N.T  0.000000000 -0.7186853 -0.8945679 -0.5578688 -0.06778933 -0.1076146
##              13         14         15         16           17         18
## N.A -0.06778933 -0.5578688 -0.8945679 -0.7186853  0.000000000 -0.3315261
## N.C -0.21395878 -0.2181970 -0.6264306 -0.5985633 -0.207282190  0.0000000
## N.G  0.00000000 -0.6809039  0.0000000 -0.8488090 -0.165379542 -0.5264819
## N.T -0.27813239  0.0000000 -0.7491354  0.0000000  0.004345295 -0.7023137
##             19          20         21          22            23
## N.A -0.2947557 -0.10894495 -0.1281696 -0.09077066 -0.0406333798
## N.C -0.0836681 -0.08580149 -0.1663383 -0.02010472 -0.0013038695
## N.G -0.3165396 -0.18511814 -0.1167290 -0.08396657  0.0000000000
## N.T  0.0000000  0.00000000  0.0000000  0.00000000 -0.0007890804
## 
## Nucleotide beta errors:
##                1            2            3            4            5
## N.A 0.0001885460 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## N.C 0.0000000000 0.0001967433 0.0001886261 0.0003185830 0.0012401957
## N.G 0.0001962933 0.0001506427 0.0002364037 0.0001569924 0.0001311099
## N.T 0.0002125932 0.0001875481 0.0001695540 0.0001545749 0.0006278464
##               6            7          8          9          10
## N.A 0.026064573 0.0001105268 0.00000000 0.03227511 0.000000000
## N.C 0.020268780 0.0002937842 0.06250011 0.00000000 0.024514816
## N.G 0.000000000 0.0003988833 0.01262749 0.02405663 0.000318178
## N.T 0.001156562 0.0000000000 0.01884502 0.05103122 0.004788921
##               11           12           13          14         15
## N.A 0.0004214464 0.0001777585 0.0001205124 0.004788921 0.05103122
## N.C 0.0000000000 0.0000000000 0.0003267171 0.000318178 0.02405663
## N.G 0.0003267171 0.0000000000 0.0000000000 0.024514816 0.00000000
## N.T 0.0001205124 0.0001777585 0.0004214464 0.000000000 0.03227511
##             16           17          18           19           20
## N.A 0.01884502 0.0000000000 0.001156562 0.0006278464 0.0001545749
## N.C 0.01262749 0.0003988833 0.000000000 0.0001311099 0.0001569924
## N.G 0.06250011 0.0002937842 0.020268780 0.0012401957 0.0003185830
## N.T 0.00000000 0.0001105268 0.026064573 0.0000000000 0.0000000000
##               21           22           23
## N.A 0.0001695540 0.0001875481 0.0002125932
## N.C 0.0002364037 0.0001506427 0.0001962933
## N.G 0.0001886261 0.0001967433 0.0000000000
## N.T 0.0000000000 0.0000000000 0.0001885460
## 
## 
## An object of class 'Intercept'
## Fits 11 views and 1 round(s) (round = 8).
## Intercept beta values:
## Round.8:
##              View.1   View.2  View.3   View.4   View.5   View.6  View.7
## StrandView 36.66482 36.76563 36.7801 36.74052 36.72631 36.75487 36.7491
##              View.8  View.9  View.10  View.11
## StrandView 36.73061 36.6779 36.69859 36.79661
## 
## Intercept beta errors:
## Round.8:
##                 View.1      View.2      View.3      View.4      View.5
## StrandView 0.003406929 0.002578573 0.002554267 0.002556745 0.002531074
##                 View.6      View.7      View.8      View.9     View.10
## StrandView 0.002532108 0.002535714 0.002516195 0.002540003 0.002576212
##                View.11
## StrandView 0.002599008
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 23.
## [1] "Number of Observations in Design Matrix: 999457"
## No shape parameters included in fit.
## [1] "i = 4"
## [1] "Round summary: "
##            8  Total
## Round 999457 999457
## [1] "Mono-nucleotide summary: "
##        N.A     N.C     N.G    N.T
## 1   583111  638672  349310 427821
## 2   719228  470663  372524 436499
## 3   910003  500114  170872 417925
## 4   928085  254654  407543 408632
## 5  1290797   18281  647468  42368
## 6      637     257 1982657  15363
## 7   843262  104878   93726 957048
## 8  1996456     416    1138    904
## 9      578 1997364     377    595
## 10 1880158     667  115091   2998
## 11   80253 1114736  111719 692206
## 12  343363  656094       0      0
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 View.8 View.9
## Strand.F   5127  64607  97215  69977 107444 129526 141257 154188 111093
## Strand.R      0      0      0      0      0      0      0      0      0
##          View.10 View.11 StrandTotal
## Strand.F   56898   62125      999457
## Strand.R       0       0           0
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+N.A1+N.G1+N.T1+N.C2+N.G2+N.T2+N.C3+N.G3+N.T3+N.C4+N.G4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.T6+N.A7+N.C7+N.G7+N.C8+N.G8+N.T8+N.A9+N.G9+N.T9+N.C10+N.G10+N.T10+N.A11+N.G11+N.T11+N.A12+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F9+Strand.F10+Strand.F11"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  AR-DBD R8 Nucleotides+View (Rev. Comp. Sym.) 
## Slot "varRegLen":  23 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATC 
## Slot "rightFixedSeq":  TGGAATTCTCGGGTGCCAAGG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.99 
## Slot "minAffinity":  0.01 
## Slot "missingValueSuppression":  0.5 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  15 
## Slot "consensusSeq":  [AG]G[AT]ACA[ACGT][ACGT][ACGT]TGT[AT]C[CT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  23 
## 
## Fits a model of footprint length 23 for mono-nucleotide features with 11 view(s) per strand of DNA and 1 round(s) of data (round = 8) with reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.8+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+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F8+Strand.F9+Strand.F10+Strand.F11 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 23 nucleotides for a feature model of length 23.
## Nucleotide features are reverse complement symmetric.
## Nucleotide beta values:
##                 1           2          3           4           5
## N.A -0.0007887409  0.00000000  0.0000000  0.00000000  0.00000000
## N.C  0.0000000000 -0.08396690 -0.1167294 -0.18511966 -0.31654095
## N.G -0.0013035035 -0.02010488 -0.1663394 -0.08580208 -0.08366877
## N.T -0.0406334158 -0.09077118 -0.1281703 -0.10894551 -0.29475700
##              6            7          8          9         10          11
## N.A -0.7023149  0.004345195  0.0000000 -0.7491367  0.0000000 -0.27813608
## N.C -0.5264832 -0.165381492 -0.8488103  0.0000000 -0.6809052  0.00000000
## N.G  0.0000000 -0.207284316 -0.5998463 -0.6311497 -0.2181994 -0.21396041
## N.T -0.3315486  0.000000000 -0.7186869 -0.9452524 -0.5578707 -0.06778956
##             12          13         14         15         16           17
## N.A -0.1076152 -0.06778956 -0.5578707 -0.9452524 -0.7186869  0.000000000
## N.C  0.0000000 -0.21396041 -0.2181994 -0.6311497 -0.5998463 -0.207284316
## N.G  0.0000000  0.00000000 -0.6809052  0.0000000 -0.8488103 -0.165381492
## N.T -0.1076152 -0.27813608  0.0000000 -0.7491367  0.0000000  0.004345195
##             18          19          20         21          22
## N.A -0.3315486 -0.29475700 -0.10894551 -0.1281703 -0.09077118
## N.C  0.0000000 -0.08366877 -0.08580208 -0.1663394 -0.02010488
## N.G -0.5264832 -0.31654095 -0.18511966 -0.1167294 -0.08396690
## N.T -0.7023149  0.00000000  0.00000000  0.0000000  0.00000000
##                23
## N.A -0.0406334158
## N.C -0.0013035035
## N.G  0.0000000000
## N.T -0.0007887409
## 
## Nucleotide beta errors:
##                1            2            3            4            5
## N.A 0.0001885461 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## N.C 0.0000000000 0.0001967433 0.0001886260 0.0003185838 0.0012401957
## N.G 0.0001962934 0.0001506428 0.0002364040 0.0001569925 0.0001311100
## N.T 0.0002125934 0.0001875482 0.0001695541 0.0001545749 0.0006278464
##               6            7          8          9           10
## N.A 0.026064573 0.0001105268 0.00000000 0.03227511 0.0000000000
## N.C 0.020267419 0.0002937855 0.06250011 0.00000000 0.0245148161
## N.G 0.000000000 0.0003988850 0.01269241 0.02451494 0.0003181797
## N.T 0.001156658 0.0000000000 0.01884502 0.06250015 0.0047889212
##               11           12           13           14         15
## N.A 0.0004214505 0.0001777585 0.0001205123 0.0047889212 0.06250015
## N.C 0.0000000000 0.0000000000 0.0003267180 0.0003181797 0.02451494
## N.G 0.0003267180 0.0000000000 0.0000000000 0.0245148161 0.00000000
## N.T 0.0001205123 0.0001777585 0.0004214505 0.0000000000 0.03227511
##             16           17          18           19           20
## N.A 0.01884502 0.0000000000 0.001156658 0.0006278464 0.0001545749
## N.C 0.01269241 0.0003988850 0.000000000 0.0001311100 0.0001569925
## N.G 0.06250011 0.0002937855 0.020267419 0.0012401957 0.0003185838
## N.T 0.00000000 0.0001105268 0.026064573 0.0000000000 0.0000000000
##               21           22           23
## N.A 0.0001695541 0.0001875482 0.0002125934
## N.C 0.0002364040 0.0001506428 0.0001962934
## N.G 0.0001886260 0.0001967433 0.0000000000
## N.T 0.0000000000 0.0000000000 0.0001885461
## 
## 
## An object of class 'Intercept'
## Fits 11 views and 1 round(s) (round = 8).
## Intercept beta values:
## Round.8:
##              View.1   View.2   View.3   View.4   View.5  View.6   View.7
## StrandView 36.66485 36.76565 36.78012 36.74055 36.72633 36.7549 36.74912
##              View.8   View.9  View.10  View.11
## StrandView 36.73063 36.67792 36.69861 36.79663
## 
## Intercept beta errors:
## Round.8:
##                 View.1      View.2      View.3      View.4      View.5
## StrandView 0.003406927 0.002578571 0.002554265 0.002556742 0.002531071
##                 View.6      View.7      View.8      View.9     View.10
## StrandView 0.002532106 0.002535712 0.002516193 0.002540001 0.002576209
##                View.11
## StrandView 0.002599006
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 23.
## [1] "Number of Observations in Design Matrix: 999455"
## No shape parameters included in fit.
## [1] "i = 5"
## [1] "Round summary: "
##            8  Total
## Round 999455 999455
## [1] "Mono-nucleotide summary: "
##        N.A     N.C     N.G    N.T
## 1   583109  638672  349310 427819
## 2   719228  470661  372522 436499
## 3   910001  500112  170872 417925
## 4   928083  254653  407543 408631
## 5  1290796   18279  647467  42368
## 6      637     257 1982654  15362
## 7   843262  104877   93725 957046
## 8  1996454     416    1137    903
## 9      578 1997362     377    593
## 10 1880157     667  115090   2996
## 11   80252 1114733  111719 692206
## 12  343362  656093       0      0
## [1] "View/strand orientation summary: "
##          View.1 View.2 View.3 View.4 View.5 View.6 View.7 View.8 View.9
## Strand.F   5127  64607  97215  69976 107444 129525 141257 154188 111093
## Strand.R      0      0      0      0      0      0      0      0      0
##          View.10 View.11 StrandTotal
## Strand.F   56898   62125      999455
## Strand.R       0       0           0
## [1] "Regression Formula: "
## [1] "ObservedCount ~ offset(logProb)+N.A1+N.G1+N.T1+N.C2+N.G2+N.T2+N.C3+N.G3+N.T3+N.C4+N.G4+N.T4+N.C5+N.G5+N.T5+N.A6+N.C6+N.T6+N.A7+N.C7+N.G7+N.C8+N.G8+N.T8+N.A9+N.G9+N.T9+N.C10+N.G10+N.T10+N.A11+N.G11+N.T11+N.A12+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F9+Strand.F10+Strand.F11"
## No shape parameters included in fit.
## An object of class 'model'
## 
## Slot "name":  AR-DBD R8 Nucleotides+View (Rev. Comp. Sym.) 
## Slot "varRegLen":  23 
## Slot "leftFixedSeq":  GTTCAGAGTTCTACAGTCCGACGATC 
## Slot "rightFixedSeq":  TGGAATTCTCGGGTGCCAAGG 
## Slot "leftFixedSeqOverlap":  5 
## Slot "rightFixedSeqOverlap":  5 
## Slot "confidenceLevel":  0.99 
## Slot "minAffinity":  0.01 
## Slot "missingValueSuppression":  0.5 
## Slot "minSeedValue":  0.01 
## Slot "seedLen":  15 
## Slot "consensusSeq":  [AG]G[AT]ACA[ACGT][ACGT][ACGT]TGT[AT]C[CT] 
## Slot "upFootprintExtend":  4 
## Slot "downFootprintExtend":  4 
## Slot "fpLen":  23 
## 
## Fits a model of footprint length 23 for mono-nucleotide features with 11 view(s) per strand of DNA and 1 round(s) of data (round = 8) with reverse complement symmetry.
## 
## Slot "regressionFormula":  ObservedCount ~ offset(logProb)+Round.8+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+Strand.F1+Strand.F2+Strand.F3+Strand.F4+Strand.F5+Strand.F6+Strand.F7+Strand.F8+Strand.F9+Strand.F10+Strand.F11 
## 
## 
## Includes the following feature sub-classes: 
## An object of class 'N'
## Fits 23 nucleotides for a feature model of length 23.
## Nucleotide features are reverse complement symmetric.
## Nucleotide beta values:
##                 1           2          3           4           5
## N.A -0.0007887409  0.00000000  0.0000000  0.00000000  0.00000000
## N.C  0.0000000000 -0.08396690 -0.1167294 -0.18511966 -0.31654095
## N.G -0.0013035035 -0.02010488 -0.1663394 -0.08580208 -0.08366877
## N.T -0.0406334158 -0.09077118 -0.1281703 -0.10894551 -0.29475700
##              6            7          8          9         10          11
## N.A -0.7023149  0.004345195  0.0000000 -0.7491367  0.0000000 -0.27813608
## N.C -0.5264832 -0.165381492 -0.8488103  0.0000000 -0.6809052  0.00000000
## N.G  0.0000000 -0.207284316 -0.5998463 -0.6311497 -0.2181994 -0.21396041
## N.T -0.3315486  0.000000000 -0.7186869 -0.9452524 -0.5578707 -0.06778956
##             12          13         14         15         16           17
## N.A -0.1076152 -0.06778956 -0.5578707 -0.9452524 -0.7186869  0.000000000
## N.C  0.0000000 -0.21396041 -0.2181994 -0.6311497 -0.5998463 -0.207284316
## N.G  0.0000000  0.00000000 -0.6809052  0.0000000 -0.8488103 -0.165381492
## N.T -0.1076152 -0.27813608  0.0000000 -0.7491367  0.0000000  0.004345195
##             18          19          20         21          22
## N.A -0.3315486 -0.29475700 -0.10894551 -0.1281703 -0.09077118
## N.C  0.0000000 -0.08366877 -0.08580208 -0.1663394 -0.02010488
## N.G -0.5264832 -0.31654095 -0.18511966 -0.1167294 -0.08396690
## N.T -0.7023149  0.00000000  0.00000000  0.0000000  0.00000000
##                23
## N.A -0.0406334158
## N.C -0.0013035035
## N.G  0.0000000000
## N.T -0.0007887409
## 
## Nucleotide beta errors:
##                1            2            3            4            5
## N.A 0.0001885461 0.0000000000 0.0000000000 0.0000000000 0.0000000000
## N.C 0.0000000000 0.0001967433 0.0001886260 0.0003185838 0.0012401957
## N.G 0.0001962934 0.0001506428 0.0002364040 0.0001569925 0.0001311100
## N.T 0.0002125934 0.0001875482 0.0001695541 0.0001545749 0.0006278464
##               6            7          8          9           10
## N.A 0.026064573 0.0001105268 0.00000000 0.03227511 0.0000000000
## N.C 0.020267181 0.0002937855 0.06250011 0.00000000 0.0245148161
## N.G 0.000000000 0.0003988850 0.01269241 0.02451494 0.0003181797
## N.T 0.001156658 0.0000000000 0.01884502 0.06250015 0.0047889212
##               11           12           13           14         15
## N.A 0.0004214505 0.0001777585 0.0001205123 0.0047889212 0.06250015
## N.C 0.0000000000 0.0000000000 0.0003267180 0.0003181797 0.02451494
## N.G 0.0003267180 0.0000000000 0.0000000000 0.0245148161 0.00000000
## N.T 0.0001205123 0.0001777585 0.0004214505 0.0000000000 0.03227511
##             16           17          18           19           20
## N.A 0.01884502 0.0000000000 0.001156658 0.0006278464 0.0001545749
## N.C 0.01269241 0.0003988850 0.000000000 0.0001311100 0.0001569925
## N.G 0.06250011 0.0002937855 0.020267181 0.0012401957 0.0003185838
## N.T 0.00000000 0.0001105268 0.026064573 0.0000000000 0.0000000000
##               21           22           23
## N.A 0.0001695541 0.0001875482 0.0002125934
## N.C 0.0002364040 0.0001506428 0.0001962934
## N.G 0.0001886260 0.0001967433 0.0000000000
## N.T 0.0000000000 0.0000000000 0.0001885461
## 
## 
## An object of class 'Intercept'
## Fits 11 views and 1 round(s) (round = 8).
## Intercept beta values:
## Round.8:
##              View.1   View.2   View.3   View.4   View.5  View.6   View.7
## StrandView 36.66485 36.76565 36.78012 36.74055 36.72633 36.7549 36.74912
##              View.8   View.9  View.10  View.11
## StrandView 36.73063 36.67792 36.69861 36.79663
## 
## Intercept beta errors:
## Round.8:
##                 View.1      View.2      View.3      View.4      View.5
## StrandView 0.003406927 0.002578571 0.002554265 0.002556742 0.002531071
##                 View.6      View.7      View.8      View.9     View.10
## StrandView 0.002532106 0.002535712 0.002516193 0.002540001 0.002576209
##                View.11
## StrandView 0.002599006
## 
## 
## 
## An object of class 'Shape'
## Fits 0 shape coefficients for 0 kinds of shape parameter(s) (shape = ) for a feature model of length 23.
## [1] "Number of Observations in Design Matrix: 999455"
## No shape parameters included in fit.
## [1] "Stability Reached after 5 iterations."
ModelTest <- finalizeFeatureBetas(ModelTest)

pM <- plot(ModelTest, plotTitle = "AR-DBD R8 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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