Nothing
QuanGR <- function(GR, method="sum", Quan="counts", by="gene_id"){
METHODS <- c("RPKM", "sum", "mean", "median", "max", "min")
idx <- pmatch(method, METHODS)
qidx <- pmatch(Quan, colnames(GR@elementMetadata))
gidx <- pmatch(by, colnames(GR@elementMetadata))
if(is.na(qidx)){
stop(paste(Quan, "is not available"))
}
RPKM <- function(GR){
N <- sum(GR@elementMetadata[,qidx])
C <- tapply(GR@elementMetadata[,qidx], GR@elementMetadata[,gidx], sum)
L <- tapply(width(GR), GR@elementMetadata[,gidx], sum)
rpkm <- (10^9*C)/(N*L)
return(rpkm)
}
if(is.na(idx)){
stop("invalid method")
}else if(idx==1){
quan <- RPKM(GR)
}else{
quan <- tapply(GR@elementMetadata[,qidx], GR@elementMetadata[,gidx], METHODS[idx])
}
quan <- cbind(quan)
colnames(quan) <- paste(METHODS[idx], "_", Quan, sep="")
return(cbind(quan))
}
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