lognormCounts.R

#' Title
#'
#' @param x
#' @param log
#' @param prior.count
#' @param lib.size
#'
#' @return
#' @export
#'
#' @examples
lognormCounts <- function(x, log = TRUE, prior.count = 0.5)
  # Function to log normalise a counts matrix to median library size
  # Input is counts matrix
  # Genes as rows, cells as columns
  # Belinda Phipson
  # 26 February 2020
{
  x <- as.matrix(x)
  lib.size <- colSums(x)
  M <- median(lib.size)
  if(log){
    prior.count.scaled <- lib.size/mean(lib.size)*prior.count
    lib.size <- lib.size + 2*prior.count.scaled
    log2(t((t(x)+prior.count.scaled)/lib.size*M))
  }
  else t(t(x)/lib.size*M)
}