Nothing
setMethod("qPCRBoxWhisker", signature = "qPCRBatch", definition =
function(qPCRBatch, cutOff = 40, statType = "parametric", plotType = "sample") {
if (statType == "parametric" || statType == "non-parametric") {
}
else {
stop("Invalid statType argument, please use \"parametric\" or \"non-parametric\"")
}
ctsMat <- exprs(qPCRBatch)
ctsMat[is.na(ctsMat)] <- cutOff # Cutoff point..Could change for different platforms
ctsMat[ctsMat > cutOff] <- cutOff
orderMat <- exprs.well.order(qPCRBatch)
plateVec <- as.vector(gsub("-.*", "", orderMat))
wellVec <- as.numeric(gsub(".*-", "", orderMat))
if(plotType == "sample") {
valueVector <- vector(length = length(ctsMat))
sampleNameVec <- vector(length = length(ctsMat))
i <- 1
sampleLength <- dim(ctsMat)[1]
cat("LENGTH IS:",sampleLength,"\n")
for(sample in colnames(ctsMat)) {
cat("SAMPLE IS",sample,"\n")
cat("I IS ", i, "\n")
valueVector[i:(i + sampleLength - 1)] <- ctsMat[,colnames(ctsMat) %in% sample]
sampleNameVec[i:(i + sampleLength -1)] <- rep(sample, sampleLength)
i <- i + sampleLength
}
cat(sampleNameVec,"\n\n")
sampleNameVec <- factor(sampleNameVec)
cat(valueVector,"\n")
graphMaker <- cbind(valueVector, sampleNameVec)
boxplot(valueVector~sampleNameVec, data = graphMaker, names=colnames(ctsMat), col="bisque")
}
if(plotType == "plate") {
valueVector <- vector(length = length(ctsMat))
plateNameVec <- vector(length = length(ctsMat))
i <- 1
plateLength <- max(wellVec)
cat("\nplateLength is:",plateLength,"\n")
for(plate in levels(factor(plateVec))) {
cat("I is ", i, "\n")
valueVector[i:(i + plateLength - 1)] <- ctsMat[plateVec == plate]
plateNameVec[i:(i + plateLength -1)] <- rep(plate, plateLength)
i <- i + plateLength
}
plateNameVec <- factor(plateNameVec)
graphMaker <- cbind(valueVector, plateNameVec)
print(graphMaker)
boxplot(valueVector~plateNameVec, data = graphMaker, names=levels(plateVec), col="bisque")
}
}
)
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