R/GetRA.R

In MicrobiomeSurv: Biomarker Validation for Microbiome-Based Survival Classification and Prediction

#' This function convert OTU matrix to RA matrix.

#'@param Micro.mat an OTU matrix with OTUs in rows and subjects in columns.
#'@return A relative abundance matrix of OTUs
#' \item{ra}{Relative abundance matrixs}

#' @author Thi Huyen Nguyen, \email{thihuyen.nguyen@@uhasselt.be}
#' @author Olajumoke Evangelina Owokotomo, \email{olajumoke.x.owokotomo@@gsk.com}
#' @author Ziv Shkedy
#' @seealso \code{\link[MicrobiomeSurv]{GetRA}}
#' @examples
#' # Read dataset
#' data(Week3_otu)
#' Week3_otu = data.frame(Week3_otu)
#' otu_mat_w3 = t(data.matrix(Week3_otu[ , 1:2720]))
#'
#' # Convert absolute abundance to relative abundance
#' ra_otu_trim_w3 = GetRA(Micro.mat = otu_mat_w3)

#' @import stats


#' @export GetRA



GetRA = function(Micro.mat) {

  ra = matrix(0,nrow(Micro.mat),ncol(Micro.mat))
  rownames(ra) = rownames(Micro.mat)
  colnames(ra) = colnames(Micro.mat)

  for(i in 1:ncol(Micro.mat)){

    if(sum(Micro.mat[,i]) == 0){
      ra[,i] = 0
    } else {
      ra[,i] = Micro.mat[,i]/sum(Micro.mat[,i])
    }

  }

  return(ra)
}