R/older_funcs/tpm.R

In IMBEIbioinformatics/BIUMmisc: A collection of functions and scripts commonly used by the BIUM-MZ Core Facility and the Bioinformatics group at the IMBEI

#' #' Title
#' #'
#' #' @param counts
#' #' @param lengths
#' #'
#' #' @return
#' #' @export
#' #'
#' #' @examples
#' tpm_diy <- function(counts, lengths) {
#'   tpm_fun <- function(counts, lengths) {
#'     rpk <- counts/(lengths/1000)
#'     coef <- sum(rpk) / 1e6
#'     rpk/coef
#'   }
#'   tpms <- apply(counts, 2, function(x) tpm_fun(x, lengths) )
#'   colnames(tpms) <- colnames(counts)
#'   rownames(tpms) <- rownames(counts)
#'   return(as.data.frame(tpms))
#' }
#'