R/obtCorMatsBatch.R

In CenterForStatistics-UGent/SPsimSeq: Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

#' A function to obtain copulas or uniform random variables
#'
#' @param cpm.data the transformed data matrix
#' @param batch the batch indicators
#' @param genewiseCor logical, whther gene wise correlation needs to be simulated
#'
#' @return The estimated correlation matrices per batch
#' @importFrom WGCNA cor
#' @importFrom limma voom
obtCorMatsBatch <- function(cpm.data, batch, genewiseCor){
  if(is.null(colnames(cpm.data))){
    vec.columns = seq_len(ncol(cpm.data))
  }else{
    vec.columns = colnames(cpm.data)
  }

  if(is.null(rownames(cpm.data))){
    vec.rows = seq_len(nrow(cpm.data))
  }else{
    vec.rows = rownames(cpm.data)
  }
  
  tapply(vec.columns, batch,  function(coln){ 
    if(genewiseCor){
      data <- cpm.data[, coln]
      voom.res <- limma::voom(data)
      W <- voom.res$weights
      WGCNA::cor(x=t(data), weights.x = t(W), use = "pairwise.complete.obs")
    }else{
      data <- cpm.data[, coln]
      cormat <- diag(x=1, nrow = nrow(data))
      rownames(cormat) <- vec.columns <- vec.rows
      cormat
    } 
  }) 
}