R/pipeline_wrappers.R

In lefeverde/basicOmics: Package for basic statistical tests on Omics data

#' Wrapper function to create dge from txi
#'
#' Wrapper which returns a dge that has been filtered
#' and is ready for downstream processing. I've
#' added a bunch of errors here which should prevent
#' mistakes in creating/using this object
#'
#' @param txi 'lengthScaledTPM' txi object
#' @param p data.frame of sample phenodata
#' @param gene_annots gene annotations
#'
#' @return DGE object
#' @export
#'
#' @examples
dge_wrapper <- function(txi, p, gene_annots){
  #TODO Error messages don't output if condition
  # need to fix that
  if(all(colnames(txi$counts) != row.names(p))){
    stop(call. = TRUE)
  }
  if(! all(row.names(txi$counts) %in% row.names(gene_annots))){
    stop(call. = TRUE)
  }

  dge <- edgeR::DGEList(counts =  txi$counts, samples = p, genes = gene_annots[row.names(txi$counts),])
  dge <- dge[edgeR::filterByExpr(dge, group = dge$samples$group),]
  dge <- dge[(rowSums(dge$counts > 1) >= .75*dim(dge)[2]),]
  dge <- dge[!is.na(dge$genes$entrezgene),] %>%
    edgeR::calcNormFactors(.)
  return(dge)

}

#' Runs voom to sva pipeline
#'
#' This runs the voom to sva pipeline then voom
#' again pipeline. Returns a voom transformed
#' object fitted with the surrogate variables
#'
#' @param dge DGE object
#' @param mod model.matrix with variables of interest
#' @param mod0 model.matrix without variables of interest
#'
#' @return voom object
#' @export
#'
#' @examples
voom_sva_wrapper <- function(dge, mod, mod0){
  v <- voom(dge, design = mod)
  # v_qa <- voomWithQualityWeights(dge,design = mod)
  svobj <- sva(v$E, mod=mod, mod0=mod0)
  modSV <- cbind(mod, svobj$sv)
  v_sv <- voom(dge, design = modSV)
  return(v_sv)

}