#' readFC read a featureCount File
#'
#' @param filename name of feature counts output file
#' @param exons boolean if features are exons and there will be duplicate gene ids
#'
#' @export
readFC <- function(filename, exons=F,name=gsub("[.]bam$","",basename(filename))){
dat <- read.delim(filename,head=T,skip=1,sep="\t")
if(exons){
rownames(dat) <- gsub(" ","",apply(dat[,c(1:4)],1,paste,collapse="_"))
}else{
rownames(dat) <- dat[,1]
}
annotation <- dat[,1:6]
counts <- as.data.frame(dat[,7:ncol(dat)])
colnames(counts) <- gsub("[.]bam$","",basename(colnames(dat)[7:ncol(dat)]))
rownames(counts) <- rownames(dat)
rownames(annotation) <- rownames(dat)
if(file.exists(paste0(filename,".summary"))){
sumDat <- read.delim(paste0(filename,".summary"), sep="\t",h=T)
sumRet <- as.data.frame(sumDat[,-1])
rownames(sumRet) <- sumDat$Status
colnames(sumRet) <- gsub("[.]bam$","",basename(colnames(sumDat)[-1]))
}else{
sumDat <- NULL
}
list(counts=counts,annotation=annotation[,-1],summary=sumDat)
}
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