Entering edit mode
6.3 years ago
firestar
★
1.6k
Can someone verify if this R code for converting raw counts to TPM is correct?
#' @title Compute TPM for a read count matrix
#' @param dfr A numeric data.frame of read counts with samples (columns) and genes (rows).
#' @param len A vector of gene cds length equal to number of rows of dfr.
#'
r_tpm <- function(dfr,len)
{
dfr1 <- sweep(dfr,MARGIN=1,(len/10^4),`/`)
scf <- colSums(dfr1)/(10^6)
return(sweep(dfr1,2,scf,`/`))
}
Do you have a reason for suspecting it's not? Have you tested it? What do your tests reveal?