R/AllShowMethods.R
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites
##############################################
############# S4 Methods #############
##############################################
########### Show Methods ##########
setMethod("show",
signature = "genomicProfiles",
definition = function(object){
widthDisplay<-round(options()$width*0.75)
if(object@tags == "empty"){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object with no internal data")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
slots <- slotNames(object)[1:4]
line1<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[1]))),collapse=''),
slots[1],"\n")
line2<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[2]))),collapse=''),
slots[2],"\n")
line3<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[3]))),collapse=''),
slots[3],"\n")
line4<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[4]))),collapse=''),
slots[4],"\n")
cat("",line1,line2,line3,line4)
}else if(object@tags == "PWM_stage"){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: Position Weight Matrix")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
bpf <- object@BPFrequency
names(bpf)<-c("A" ,"C" ,"G" ,"T")
cat("Position Weight Matrix (PWM): \n","\n")
print(object@PWM)
cat(rep("_", widthDisplay),"\n","\n")
cat("Base pairs frequency for PWM weighting : \n","\n")
print(bpf)
cat(rep("_", widthDisplay),"\n","\n")
cat("PWM built from (PFM - Format ",object@PFMFormat, ") : \n","\n")
print(object@PFM)
cat("\n",rep("_", widthDisplay),"\n")
}else if(grepl("genomeWide",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
if(grepl("CS",object@tags)){
title <- as.character("genomicProfiles object: Accessible Chromatin Score")
} else{
title <- as.character("genomicProfiles object: Genome Wide Score")
}
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("","Position Weight Matrix (PWM): \n","\n")
print(object@PWM)
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("maxPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("maxPWMScore: ")-nchar(object@maxPWMScore))),collapse=''),
object@maxPWMScore,"\n"))
cat("",paste0("minPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("minPWMScore: ")-nchar(object@minPWMScore))),collapse=''),
object@minPWMScore,"\n"))
cat("",paste0("averageExpPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("averageExpPWMScore: ")-nchar(paste0(object@averageExpPWMScore[1],"(lambda = ",object@lambdaPWM[1],")")))),collapse=''),
object@averageExpPWMScore," (lambda = ",object@lambdaPWM,")\n"))
cat("",paste0("DNASequenceLength: ",paste(rep(" ",
times=(widthDisplay-nchar("DNASequenceLength: ")-nchar(object@DNASequenceLength))),collapse=''),
object@DNASequenceLength,"\n"))
cat(rep("_", widthDisplay),"\n","\n")
}else if(grepl("PWMScore",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: PWM scores above Threshold")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
if(length(profile)<2){
cat("","Scores above Threshold in locus: ","\n")
print(profile)
}else{
cat("","Scores above Threshold in locus: ","\n")
print(profile[[1]])
cat("\n")
cat("",length(profile)-1," remaining loci","\n")
cat("",paste0("Locus: ",paste(rep(" ",
times=(widthDisplay-nchar("Locus: ")-nchar(paste0(names(profile)[1],"(length = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (length = ",sapply(profile, length)[2:length(profile)],")\n"))
}
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("Associated parameters")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("minPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("minPWMScore: ")-nchar(object@minPWMScore))),collapse=''),
object@minPWMScore,"\n"))
cat("",paste0("maxPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("minPWMScore: ")-nchar(object@maxPWMScore))),collapse=''),
object@maxPWMScore,"\n"))
cat("",paste0("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n"))
cat("",paste0("PWMThreshold: ",paste(rep(" ",
times=(widthDisplay-nchar("PWMThreshold: ")-nchar(object@PWMThreshold))),collapse=''),
object@PWMThreshold,"\n"))
}else if(grepl("Occupancy",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: Occupancy at sites above Threshold")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
if(length(profile)<2){
cat("","Parameter combination: ",names(profile),"\n","\n")
print(profile)
}else{
cat("","Parameter combination: ",names(profile)[1],"\n","\n")
print(profile[[1]])
cat("\n")
cat("",length(profile)-1," remaining combinations","\n","\n")
cat("",paste0("Parameter combination: ",paste(rep(" ",
times=(widthDisplay-nchar(paste0(names(profile)[1],"(loci = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (loci = ",sapply(profile, length)[2:length(profile)],")\n"))
}
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("Associated parameters")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n"))
cat("",paste0("boundMolecules: ",paste(rep(" ",
times=(widthDisplay-nchar("boundMolecules: ")-nchar(object@boundMolecules[1]))),collapse=''),
object@boundMolecules,"\n"))
}else if(grepl("ChIPProfile",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: ChIP like Profiles")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
if(length(profile)<2){
cat("","Parameter combination: ",names(profile),"\n","\n")
print(profile)
}else{
cat("","Parameter combination: ",names(profile)[1],"\n","\n")
print(profile[[1]])
cat("\n")
cat("",length(profile)-1," remaining combinations","\n","\n")
cat("",paste0("Parameter combination: ",paste(rep(" ",
times=(widthDisplay-nchar(paste0(names(profile)[1],"(loci = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (loci = ",sapply(profile, length)[2:length(profile)],")\n"))
}
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("Associated parameter Options")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n"))
cat("",paste0("boundMolecules: ",paste(rep(" ",
times=(widthDisplay-nchar("boundMolecules: ")-nchar(object@boundMolecules[1]))),collapse=''),
object@boundMolecules,"\n"))
cat("",paste0("stepSize: ",paste(rep(" ",
times=(widthDisplay-nchar("stepSize: ")-nchar(object@stepSize))),collapse=''),
object@stepSize,"\n"))
cat("",paste0("backgroundSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("backgroundSignal: ")-nchar(object@backgroundSignal))),collapse=''),
object@backgroundSignal,"\n"))
cat("",paste0("maxSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("maxSignal: ")-nchar(object@maxSignal))),collapse=''),
object@maxSignal,"\n"))
cat("",paste0("removeBackground: ",paste(rep(" ",
times=(widthDisplay-nchar("removeBackground: ")-nchar(object@removeBackground))),collapse=''),
object@removeBackground,"\n"))
cat("",paste0("chipMean: ",paste(rep(" ",
times=(widthDisplay-nchar("chipMean: ")-nchar(object@chipMean))),collapse=''),
object@chipMean,"\n"))
cat("",paste0("chipSd: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSd: ")-nchar(object@chipSd))),collapse=''),
object@chipSd,"\n"))
cat("",paste0("chipSmooth: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSmooth: ")-nchar(object@chipSmooth))),collapse=''),
object@chipSmooth,"\n"))
} else if(grepl("GoF",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: Goodness of Fit ")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
metrics<- names(profile[[1]][[1]])[!grepl("Mean",names(profile[[1]][[1]]))]
cat("","Selected Goodness of Fit metrics: ","\n")
for(i in seq_along(metrics)){
cat("",metrics[i],"\n")
}
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste(length(profile),"parameter combinations for",length(profile[[1]]),"loci"),"\n")
cat(rep("_", widthDisplay),"\n","\n")
if(length(profile)<2){
cat("","Parameter combination: ",names(profile),"\n","\n")
print(profile[[1]][[1]][grep("Mean",names(profile[[1]][[1]]))])
cat("\n",paste(names(profile[[1]]),"\n"))
cat("\n")
cat(rep("_", widthDisplay),"\n","\n")
}else{
cat("","Parameter combination: ",names(profile)[1],"\n","\n")
print(profile[[1]][[1]][grep("Mean",names(profile[[1]][[1]]))])
cat("\n",paste(names(profile[[1]]),"\n"))
cat("\n")
cat("",length(profile)-1," remaining combinations","\n","\n")
cat("",paste0("Parameter combination: ",paste(rep(" ",
times=(widthDisplay-nchar(paste0(names(profile)[1],"(loci = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (loci = ",sapply(profile, length)[2:length(profile)],")\n"))
cat(rep("_", widthDisplay),"\n","\n")
}
}
}
)
setMethod("show",
signature = "parameterOptions",
definition = function(object){
widthDisplay<-round(options()$width*0.75)
line1<-class(object)
line2<-paste("Ploidy: ",paste(rep(" ",
times=(widthDisplay-nchar("Ploidy: ")-nchar(object@ploidy))),collapse=''),
object@ploidy,"\n")
line3<-paste("boundMolecules: ",paste(rep(" ",
times=(widthDisplay-nchar("boundMolecules: ")-nchar(object@boundMolecules[1]))),collapse=''),
object@boundMolecules,"\n")
line4<-paste("maxSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("maxSignal: ")-nchar(object@maxSignal))),collapse=''),
object@maxSignal,"\n")
line5<-paste("backgroundSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("backgroundSignal: ")-nchar(object@backgroundSignal))),collapse=''),
object@backgroundSignal,"\n")
line6<-paste("chipMean: ",paste(rep(" ",
times=(widthDisplay-nchar("chipMean: ")-nchar(object@chipMean))),collapse=''),
object@chipMean,"\n")
line7<-paste("chipSd: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSd: ")-nchar(object@chipSd))),collapse=''),
object@chipSd,"\n")
line8<-paste("chipSmooth:",paste(rep(" ",
times=(widthDisplay-nchar("chipSmooth:")-nchar(object@chipSmooth))),collapse=''),
object@chipSmooth,"\n")
line9<-paste("stepSize: ",paste(rep(" ",
times=(widthDisplay-nchar("StepSize: ")-nchar(object@stepSize))),collapse=''),
object@stepSize,"\n")
line10<-paste("lociWidth: ",paste(rep(" ",
times=(widthDisplay-nchar("lociWidth: ")-nchar(object@lociWidth))),collapse=''),
object@lociWidth,"\n")
line11<-paste("removeBackground: ",paste(rep(" ",
times=(widthDisplay-nchar("removeBackground: ")-nchar(object@removeBackground))),collapse=''),
object@removeBackground,"\n")
line12<-paste("noiseFilter: ",paste(rep(" ",
times=(widthDisplay-nchar("noiseFilter: ")-nchar(object@noiseFilter))),collapse=''),
object@noiseFilter,"\n")
line13<-paste("naturalLog: ",paste(rep(" ",
times=(widthDisplay-nchar("naturalLog: ")-nchar(object@naturalLog))),collapse=''),
object@naturalLog,"\n")
line14<-paste("noOfSites: ",paste(rep(" ",
times=(widthDisplay-nchar("noOfSites: ")-nchar(object@noOfSites))),collapse=''),
object@noOfSites,"\n")
line15<-paste("PWMThreshold: ",paste(rep(" ",
times=(widthDisplay-nchar("PWMThreshold: ")-nchar(object@PWMThreshold))),collapse=''),
object@PWMThreshold,"\n")
line16<-paste("strandRule: ",paste(rep(" ",
times=(widthDisplay-nchar("strandRule: ")-nchar(object@strandRule))),collapse=''),
object@strandRule,"\n")
line17<-paste("whichstrand: ",paste(rep(" ",
times=(widthDisplay-nchar("whichstrand: ")-nchar(object@whichstrand))),collapse=''),
object@whichstrand,"\n")
line18<-paste("PWMpseudocount: ",paste(rep(" ",
times=(widthDisplay-nchar("PWMpseudocount: ")-nchar(object@PWMpseudocount))),collapse=''),
object@PWMpseudocount,"\n")
line19<-paste("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n")
### conditional prinint
if(object@paramTag=="empty"){
cat(rep("_", widthDisplay),"\n")
title <- line1
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("processingChIP options","\n","\n"),line6,line7,
line8, line10,line12,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("processingChIP options Updated","\n","\n"),line4,line5,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("Position Weight Matrix Options","\n","\n"),line13,line14,line18,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("Genome Wide Score options","\n","\n"),line16,line17,line19,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("PWM Scores above Threshold options","\n","\n"),line16,line17,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("Occupancy options","\n","\n"),line2,line19,line3,line4,line5,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("ChIP Profile options","\n","\n"),line6,line7,line8,line9,"\n")
cat(rep("_", widthDisplay),"\n")
}
}
)
setMethod("show",
signature = "ChIPScore",
definition = function(object){
widthDisplay<-round(options()$width*0.75)
scores<-object@scores
cat(rep("_", widthDisplay),"\n")
title <- as.character(paste("ChIP score from", length(scores),"regions"))
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
if(length(scores)>6){
topScore <- c(paste(round(scores[[1]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[2]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[3]][1:6],digits=3),sep='',collapse=' '))
len<-length(scores)
bottomScore <- c(paste(round(scores[[len-2]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[len-1]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[len]][1:6],digits=3),sep='',collapse=' '))
cat("",paste("[",1:3,"] ",head(names(scores),3)," : ",topScore,"...\n"),
paste(" . . .","\n"),
paste(" . . .","\n"),
paste(" . . .","\n"),
paste("[",(len-2):len,"] ",tail(names(scores),3)," : ",bottomScore,"...\n")
)
} else{
cat(paste("[",seq_along(scores),"] ",names(scores)),"\n")
}
cat(rep("_", widthDisplay),"\n","\n")
cat(rep("_", widthDisplay),"\n","\n")
title <- paste("Top ", length(object@loci)," regions")
titleWidth<-nchar(title, type="char")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
print(object@loci)
cat(rep("_", widthDisplay),"\n","\n")
cat(rep("_", widthDisplay),"\n","\n")
title <- "Associated Options"
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
line<-paste("","backgroundSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("backgroundSignal: ")-nchar(object@backgroundSignal))),collapse=''),
object@backgroundSignal,"\n")
line2<-paste("maxSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("maxSignal: ")-nchar(object@maxSignal))),collapse=''),
object@maxSignal,"\n")
line3<-paste("chipMean: ",paste(rep(" ",
times=(widthDisplay-nchar("chipMean: ")-nchar(object@chipMean))),collapse=''),
object@chipMean,"\n")
line4<-paste("chipSd: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSd: ")-nchar(object@chipSd))),collapse=''),
object@chipSd,"\n")
line5<-paste("chipSmooth: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSmooth: ")-nchar(object@chipSmooth))),collapse=''),
object@chipSmooth,"\n")
line6<-paste("lociWidth: ",paste(rep(" ",
times=(widthDisplay-nchar("lociWidth: ")-nchar(object@lociWidth))),collapse=''),
object@lociWidth,"\n")
cat(line,line2,line3,line4,line5,line6)
cat(rep("_", widthDisplay),"\n")
}
)
patrickCNMartin/ChIPanalyser documentation built on Nov. 24, 2022, 12:02 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
##############################################
############# S4 Methods #############
##############################################
########### Show Methods ##########
setMethod("show",
signature = "genomicProfiles",
definition = function(object){
widthDisplay<-round(options()$width*0.75)
if(object@tags == "empty"){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object with no internal data")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
slots <- slotNames(object)[1:4]
line1<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[1]))),collapse=''),
slots[1],"\n")
line2<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[2]))),collapse=''),
slots[2],"\n")
line3<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[3]))),collapse=''),
slots[3],"\n")
line4<-paste("Suggested Slots : ",paste(rep(" ",
times=(widthDisplay-nchar("Suggested Slots : ")-nchar(slots[4]))),collapse=''),
slots[4],"\n")
cat("",line1,line2,line3,line4)
}else if(object@tags == "PWM_stage"){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: Position Weight Matrix")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
bpf <- object@BPFrequency
names(bpf)<-c("A" ,"C" ,"G" ,"T")
cat("Position Weight Matrix (PWM): \n","\n")
print(object@PWM)
cat(rep("_", widthDisplay),"\n","\n")
cat("Base pairs frequency for PWM weighting : \n","\n")
print(bpf)
cat(rep("_", widthDisplay),"\n","\n")
cat("PWM built from (PFM - Format ",object@PFMFormat, ") : \n","\n")
print(object@PFM)
cat("\n",rep("_", widthDisplay),"\n")
}else if(grepl("genomeWide",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
if(grepl("CS",object@tags)){
title <- as.character("genomicProfiles object: Accessible Chromatin Score")
} else{
title <- as.character("genomicProfiles object: Genome Wide Score")
}
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("","Position Weight Matrix (PWM): \n","\n")
print(object@PWM)
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("maxPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("maxPWMScore: ")-nchar(object@maxPWMScore))),collapse=''),
object@maxPWMScore,"\n"))
cat("",paste0("minPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("minPWMScore: ")-nchar(object@minPWMScore))),collapse=''),
object@minPWMScore,"\n"))
cat("",paste0("averageExpPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("averageExpPWMScore: ")-nchar(paste0(object@averageExpPWMScore[1],"(lambda = ",object@lambdaPWM[1],")")))),collapse=''),
object@averageExpPWMScore," (lambda = ",object@lambdaPWM,")\n"))
cat("",paste0("DNASequenceLength: ",paste(rep(" ",
times=(widthDisplay-nchar("DNASequenceLength: ")-nchar(object@DNASequenceLength))),collapse=''),
object@DNASequenceLength,"\n"))
cat(rep("_", widthDisplay),"\n","\n")
}else if(grepl("PWMScore",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: PWM scores above Threshold")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
if(length(profile)<2){
cat("","Scores above Threshold in locus: ","\n")
print(profile)
}else{
cat("","Scores above Threshold in locus: ","\n")
print(profile[[1]])
cat("\n")
cat("",length(profile)-1," remaining loci","\n")
cat("",paste0("Locus: ",paste(rep(" ",
times=(widthDisplay-nchar("Locus: ")-nchar(paste0(names(profile)[1],"(length = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (length = ",sapply(profile, length)[2:length(profile)],")\n"))
}
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("Associated parameters")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("minPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("minPWMScore: ")-nchar(object@minPWMScore))),collapse=''),
object@minPWMScore,"\n"))
cat("",paste0("maxPWMScore: ",paste(rep(" ",
times=(widthDisplay-nchar("minPWMScore: ")-nchar(object@maxPWMScore))),collapse=''),
object@maxPWMScore,"\n"))
cat("",paste0("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n"))
cat("",paste0("PWMThreshold: ",paste(rep(" ",
times=(widthDisplay-nchar("PWMThreshold: ")-nchar(object@PWMThreshold))),collapse=''),
object@PWMThreshold,"\n"))
}else if(grepl("Occupancy",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: Occupancy at sites above Threshold")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
if(length(profile)<2){
cat("","Parameter combination: ",names(profile),"\n","\n")
print(profile)
}else{
cat("","Parameter combination: ",names(profile)[1],"\n","\n")
print(profile[[1]])
cat("\n")
cat("",length(profile)-1," remaining combinations","\n","\n")
cat("",paste0("Parameter combination: ",paste(rep(" ",
times=(widthDisplay-nchar(paste0(names(profile)[1],"(loci = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (loci = ",sapply(profile, length)[2:length(profile)],")\n"))
}
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("Associated parameters")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n"))
cat("",paste0("boundMolecules: ",paste(rep(" ",
times=(widthDisplay-nchar("boundMolecules: ")-nchar(object@boundMolecules[1]))),collapse=''),
object@boundMolecules,"\n"))
}else if(grepl("ChIPProfile",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: ChIP like Profiles")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
if(length(profile)<2){
cat("","Parameter combination: ",names(profile),"\n","\n")
print(profile)
}else{
cat("","Parameter combination: ",names(profile)[1],"\n","\n")
print(profile[[1]])
cat("\n")
cat("",length(profile)-1," remaining combinations","\n","\n")
cat("",paste0("Parameter combination: ",paste(rep(" ",
times=(widthDisplay-nchar(paste0(names(profile)[1],"(loci = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (loci = ",sapply(profile, length)[2:length(profile)],")\n"))
}
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("Associated parameter Options")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste0("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n"))
cat("",paste0("boundMolecules: ",paste(rep(" ",
times=(widthDisplay-nchar("boundMolecules: ")-nchar(object@boundMolecules[1]))),collapse=''),
object@boundMolecules,"\n"))
cat("",paste0("stepSize: ",paste(rep(" ",
times=(widthDisplay-nchar("stepSize: ")-nchar(object@stepSize))),collapse=''),
object@stepSize,"\n"))
cat("",paste0("backgroundSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("backgroundSignal: ")-nchar(object@backgroundSignal))),collapse=''),
object@backgroundSignal,"\n"))
cat("",paste0("maxSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("maxSignal: ")-nchar(object@maxSignal))),collapse=''),
object@maxSignal,"\n"))
cat("",paste0("removeBackground: ",paste(rep(" ",
times=(widthDisplay-nchar("removeBackground: ")-nchar(object@removeBackground))),collapse=''),
object@removeBackground,"\n"))
cat("",paste0("chipMean: ",paste(rep(" ",
times=(widthDisplay-nchar("chipMean: ")-nchar(object@chipMean))),collapse=''),
object@chipMean,"\n"))
cat("",paste0("chipSd: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSd: ")-nchar(object@chipSd))),collapse=''),
object@chipSd,"\n"))
cat("",paste0("chipSmooth: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSmooth: ")-nchar(object@chipSmooth))),collapse=''),
object@chipSmooth,"\n"))
} else if(grepl("GoF",object@tags)){
cat(rep("_", widthDisplay),"\n","\n")
title <- as.character("genomicProfiles object: Goodness of Fit ")
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n","\n")
profile<-object@profiles
metrics<- names(profile[[1]][[1]])[!grepl("Mean",names(profile[[1]][[1]]))]
cat("","Selected Goodness of Fit metrics: ","\n")
for(i in seq_along(metrics)){
cat("",metrics[i],"\n")
}
cat(rep("_", widthDisplay),"\n","\n")
cat("",paste(length(profile),"parameter combinations for",length(profile[[1]]),"loci"),"\n")
cat(rep("_", widthDisplay),"\n","\n")
if(length(profile)<2){
cat("","Parameter combination: ",names(profile),"\n","\n")
print(profile[[1]][[1]][grep("Mean",names(profile[[1]][[1]]))])
cat("\n",paste(names(profile[[1]]),"\n"))
cat("\n")
cat(rep("_", widthDisplay),"\n","\n")
}else{
cat("","Parameter combination: ",names(profile)[1],"\n","\n")
print(profile[[1]][[1]][grep("Mean",names(profile[[1]][[1]]))])
cat("\n",paste(names(profile[[1]]),"\n"))
cat("\n")
cat("",length(profile)-1," remaining combinations","\n","\n")
cat("",paste0("Parameter combination: ",paste(rep(" ",
times=(widthDisplay-nchar(paste0(names(profile)[1],"(loci = ",length(profile[[1]]),")")))),collapse=''),
names(profile)[2:length(profile)]," (loci = ",sapply(profile, length)[2:length(profile)],")\n"))
cat(rep("_", widthDisplay),"\n","\n")
}
}
}
)
setMethod("show",
signature = "parameterOptions",
definition = function(object){
widthDisplay<-round(options()$width*0.75)
line1<-class(object)
line2<-paste("Ploidy: ",paste(rep(" ",
times=(widthDisplay-nchar("Ploidy: ")-nchar(object@ploidy))),collapse=''),
object@ploidy,"\n")
line3<-paste("boundMolecules: ",paste(rep(" ",
times=(widthDisplay-nchar("boundMolecules: ")-nchar(object@boundMolecules[1]))),collapse=''),
object@boundMolecules,"\n")
line4<-paste("maxSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("maxSignal: ")-nchar(object@maxSignal))),collapse=''),
object@maxSignal,"\n")
line5<-paste("backgroundSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("backgroundSignal: ")-nchar(object@backgroundSignal))),collapse=''),
object@backgroundSignal,"\n")
line6<-paste("chipMean: ",paste(rep(" ",
times=(widthDisplay-nchar("chipMean: ")-nchar(object@chipMean))),collapse=''),
object@chipMean,"\n")
line7<-paste("chipSd: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSd: ")-nchar(object@chipSd))),collapse=''),
object@chipSd,"\n")
line8<-paste("chipSmooth:",paste(rep(" ",
times=(widthDisplay-nchar("chipSmooth:")-nchar(object@chipSmooth))),collapse=''),
object@chipSmooth,"\n")
line9<-paste("stepSize: ",paste(rep(" ",
times=(widthDisplay-nchar("StepSize: ")-nchar(object@stepSize))),collapse=''),
object@stepSize,"\n")
line10<-paste("lociWidth: ",paste(rep(" ",
times=(widthDisplay-nchar("lociWidth: ")-nchar(object@lociWidth))),collapse=''),
object@lociWidth,"\n")
line11<-paste("removeBackground: ",paste(rep(" ",
times=(widthDisplay-nchar("removeBackground: ")-nchar(object@removeBackground))),collapse=''),
object@removeBackground,"\n")
line12<-paste("noiseFilter: ",paste(rep(" ",
times=(widthDisplay-nchar("noiseFilter: ")-nchar(object@noiseFilter))),collapse=''),
object@noiseFilter,"\n")
line13<-paste("naturalLog: ",paste(rep(" ",
times=(widthDisplay-nchar("naturalLog: ")-nchar(object@naturalLog))),collapse=''),
object@naturalLog,"\n")
line14<-paste("noOfSites: ",paste(rep(" ",
times=(widthDisplay-nchar("noOfSites: ")-nchar(object@noOfSites))),collapse=''),
object@noOfSites,"\n")
line15<-paste("PWMThreshold: ",paste(rep(" ",
times=(widthDisplay-nchar("PWMThreshold: ")-nchar(object@PWMThreshold))),collapse=''),
object@PWMThreshold,"\n")
line16<-paste("strandRule: ",paste(rep(" ",
times=(widthDisplay-nchar("strandRule: ")-nchar(object@strandRule))),collapse=''),
object@strandRule,"\n")
line17<-paste("whichstrand: ",paste(rep(" ",
times=(widthDisplay-nchar("whichstrand: ")-nchar(object@whichstrand))),collapse=''),
object@whichstrand,"\n")
line18<-paste("PWMpseudocount: ",paste(rep(" ",
times=(widthDisplay-nchar("PWMpseudocount: ")-nchar(object@PWMpseudocount))),collapse=''),
object@PWMpseudocount,"\n")
line19<-paste("lambdaPWM: ",paste(rep(" ",
times=(widthDisplay-nchar("lambdaPWM: ")-nchar(object@lambdaPWM[1]))),collapse=''),
object@lambdaPWM,"\n")
### conditional prinint
if(object@paramTag=="empty"){
cat(rep("_", widthDisplay),"\n")
title <- line1
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("processingChIP options","\n","\n"),line6,line7,
line8, line10,line12,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("processingChIP options Updated","\n","\n"),line4,line5,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("Position Weight Matrix Options","\n","\n"),line13,line14,line18,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("Genome Wide Score options","\n","\n"),line16,line17,line19,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("PWM Scores above Threshold options","\n","\n"),line16,line17,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("Occupancy options","\n","\n"),line2,line19,line3,line4,line5,"\n")
cat(rep("_", widthDisplay),"\n")
cat("",paste("ChIP Profile options","\n","\n"),line6,line7,line8,line9,"\n")
cat(rep("_", widthDisplay),"\n")
}
}
)
setMethod("show",
signature = "ChIPScore",
definition = function(object){
widthDisplay<-round(options()$width*0.75)
scores<-object@scores
cat(rep("_", widthDisplay),"\n")
title <- as.character(paste("ChIP score from", length(scores),"regions"))
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
if(length(scores)>6){
topScore <- c(paste(round(scores[[1]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[2]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[3]][1:6],digits=3),sep='',collapse=' '))
len<-length(scores)
bottomScore <- c(paste(round(scores[[len-2]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[len-1]][1:6],digits=3),sep='',collapse=' '),
paste(round(scores[[len]][1:6],digits=3),sep='',collapse=' '))
cat("",paste("[",1:3,"] ",head(names(scores),3)," : ",topScore,"...\n"),
paste(" . . .","\n"),
paste(" . . .","\n"),
paste(" . . .","\n"),
paste("[",(len-2):len,"] ",tail(names(scores),3)," : ",bottomScore,"...\n")
)
} else{
cat(paste("[",seq_along(scores),"] ",names(scores)),"\n")
}
cat(rep("_", widthDisplay),"\n","\n")
cat(rep("_", widthDisplay),"\n","\n")
title <- paste("Top ", length(object@loci)," regions")
titleWidth<-nchar(title, type="char")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
print(object@loci)
cat(rep("_", widthDisplay),"\n","\n")
cat(rep("_", widthDisplay),"\n","\n")
title <- "Associated Options"
titleWidth<-nchar(title, type="byte")
cat(rep(" ",ceiling((widthDisplay)/5)),title,"\n")
cat(rep("_", widthDisplay),"\n")
line<-paste("","backgroundSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("backgroundSignal: ")-nchar(object@backgroundSignal))),collapse=''),
object@backgroundSignal,"\n")
line2<-paste("maxSignal: ",paste(rep(" ",
times=(widthDisplay-nchar("maxSignal: ")-nchar(object@maxSignal))),collapse=''),
object@maxSignal,"\n")
line3<-paste("chipMean: ",paste(rep(" ",
times=(widthDisplay-nchar("chipMean: ")-nchar(object@chipMean))),collapse=''),
object@chipMean,"\n")
line4<-paste("chipSd: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSd: ")-nchar(object@chipSd))),collapse=''),
object@chipSd,"\n")
line5<-paste("chipSmooth: ",paste(rep(" ",
times=(widthDisplay-nchar("chipSmooth: ")-nchar(object@chipSmooth))),collapse=''),
object@chipSmooth,"\n")
line6<-paste("lociWidth: ",paste(rep(" ",
times=(widthDisplay-nchar("lociWidth: ")-nchar(object@lociWidth))),collapse=''),
object@lociWidth,"\n")
cat(line,line2,line3,line4,line5,line6)
cat(rep("_", widthDisplay),"\n")
}
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.