R/normalize.R

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

#' @title Normalize a matrix
#'
#' @description Normalize a matrix column-wise by dividing each entry by its corresponding column sum.
#'
#' @details Columns summing to zero are removed by default.
#'
#' @param x a matrix
#' @param removeZero remove columns summing to zero.
#' @return a normalized matrix
#' @export

normalize<-function(x, removeZero=TRUE){
  # remove columns with only zeros from matrix, to avoid dividing by a zero
  colsums = apply(x,2,sum)
  if(removeZero==TRUE){
    zero.col.indices=which(colsums==0)
    #print(length(zero.col.indices))
    if(length(zero.col.indices)>0){
      colsums=colsums[setdiff(1:ncol(x),zero.col.indices)]
      x=x[setdiff(1:ncol(x),zero.col.indices),]
    }
  }
  for(i in 1:ncol(x)){
    x[,i]=x[,i]/colsums[i]
  }
  x
}