R/rmaNormalizer.R

In YC3/mirNet: microRNA netowrk analyses

#' @title Normalize RNA-seq or miRNA-seq dataset with RMA method
#'
#' @description \code{rmaNormalizer} normalizes RNA-seq expression dataset using RMA method (without median polish step).
#'
#' @param data A data matrix, with rows referring to genes/microRNAs and columns to samples.
#'
#' @return A data matrix with normalized gene/microRNA expression data. A scatter plots of NA proportions across samples and genes/microRNAs.
#'
#' @importFrom oligo backgroundCorrect
#' @importFrom limma normalizeBetweenArrays
#' 
#' @export rmaNormalizer
#'
#' @examples
#' rmaNormalizer(data.m)


rmaNormalizer <- function(data.m){
    
    # NAs
    data.m[which(is.na(data.m), arr.ind = TRUE)] <- 0

    # RMA for background correction
    data.bg <- backgroundCorrect(data.m, method = 'rma')
    dimnames(data.bg) <- dimnames(data.m)

    # Log2 transformation
    data.bg.log <- log2(data.bg)
    print('Done log2 transformation')
    
    # quantile normalization
    data.bg.log.qn <- normalizeBetweenArrays(data.bg.log)
    print('Done quantile normalization')
    
    data.bg.log.qn
}