#'A qPCRdata function
#'
#' this is a function that makes a new qPCR object. Library "HTqPCR" needed.
#' @param
#' DataName = a string with the name of the data;
#' @param
#' ControlGene = the name of the control gene.
#'
qPCRdata<-function(DataName, ControlGene) {
object<-get(DataName)
# ind<-as.numeric(gsub("\\w+_","",DataName))
ft <- rep("Target",nrow(object))
ind<-which(rownames(object)==ControlGene)
ft[ind] <- "Endogenous Control"
fc <- matrix("OK",nrow=nrow(object),ncol=ncol(object))
fc[which(object>34.9999,arr.ind=TRUE)] <- "Undetermined"
colnames(fc) <- colnames(object)
rownames(fc) <- rownames(object)
fl <- matrix("Passed",nrow=nrow(object),ncol=ncol(object))
fl[which(object>34.9999,arr.ind=TRUE)] <- "Flagged"
colnames(fl) <- colnames(object)
rownames(fl) <- rownames(object)
TaqMan <- new("qPCRset", exprs=object, flag=fl)
featureNames(TaqMan) <- rownames(object)
featureType(TaqMan) <- ft
featureCategory(TaqMan) <- as.data.frame(fc)
sType <- c(rep("A",4),rep("B",4),rep("C",4),rep("D",4))
# PartID <- c(rep(ind, dim(object)[2]))
# tab <- data.frame(sampleName=colnames(object), sampleType=sType, dataPartID=PartID)
tab <- data.frame(sampleName=colnames(object), sampleType=sType)
phenoData(TaqMan) <- AnnotatedDataFrame(data=tab)
return(TaqMan)
}
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