R/runEdgeRNorm.R

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

### Function runEdgeRNorm ###
#' Function  runEdgeRNorm (edgeR normlization )
#'
#' Returns a DGEobj containing DGEList object representing the result of
#'  edgeR TMM normalization.
#'
#' @author John Thompson, \email{jrt@@thompsonclan.org}
#' @keywords gene symbol, Entrez, GeneID
#'
#' @param dgeObj A DGEobj data structure containing counts, design
#'    data and gene annotation
#' @param normMethod One of "TMM", "RLE", "upperquartile" or "none". Default = "TMM"
#' @param plotFile Enable a Barplot of the norm.factors produced (Default = "Norm.Factors.PNG")
#'   Set to NULL to disable the plot.
#' @param plotLabels Sample labels for the plot. Length must equal the number of
#'   samples. (Default = NULL;  sample number will be displayed)
#'
#' @return A DGEObj with a normalized DGEList added.
#'
#' @examples
#' MyDgeObj <- runEdgeRNorm (RSE)
#'
#' MyDgeObj <- runEdgeRNorm (MyDgeObj)
#'
#' @import magrittr
#' @importFrom edgeR calcNormFactors DGEList
#' @importFrom DGEobj addItem getItem
#' @importFrom assertthat assert_that
#'
#'
#' @export
runEdgeRNorm <- function(dgeObj, normMethod="TMM",
                         plotFile="TMM_Norm.Factors.PNG",
                         plotLabels = NULL){

  funArgs <- match.call()

  assertthat::assert_that ((class(dat) %in% c("DGEobj")))

  #convert counts to a matrix
  CountsMatrix = as.matrix(DGEobj::getItem(dgeObj, "counts"))

  #Now ready to normalize counts
  MyDGElist = CountsMatrix %>%
    edgeR::DGEList() %>%  #edgeR
    edgeR::calcNormFactors(method = normMethod)

  #capture the DGEList
  itemAttr <- list(normalization=normMethod)
  dgeObj <- DGEobj::addItem(dgeObj, item=MyDGElist,
                            itemName="DGEList",
                            itemType="DGEList",
                            funArgs=funArgs,
                            itemAttr=itemAttr,
                            parent="counts")

  #plot the Norm factors
  if (!is.null(plotLabels)  && length(plotLabels == ncol(dgeObj))){
    x = plotLabels
    angle = 45
  } else {
    x = 1:ncol(dgeObj)
    angle = 0
  }

  if (!is.null(plotFile)){ #barplot of norm.factors
    df <- data.frame(x = factor(x),
                     Norm.Factors = MyDGElist$samples$norm.factors)
    nfplot <- ggplot (df, aes(x=x, y=Norm.Factors)) +
                geom_bar (stat="identity", color = "dodgerblue4",
                          fill = "dodgerblue3", width = 0.7) +
                geom_hline(yintercept = 1.0, color = "red") +
                xlab("Samples") +
                ylab("Norm Factors") +
                ggtitle ("Normalization Factors") +
                theme_bw(12) +
                theme(axis.text.x = element_text(angle=angle, hjust = 1.0))

    print(nfplot)
    printAndSave (nfplot, filename = plotFile, printPlot=FALSE)

  }

  return(dgeObj)
}