R/test_diffs.R

In avastermark19/doseR_development: Test Package of doseR

#' @title test_diffs Statistics function to summarize expression data of a countData object, using ratios between selected treatments.
#' @description generateStats is a summary function used on various expression data , using ratios between selected treatments.
#' @usage test_diffs(cD, groupings, treatment1, treatment2, mode_mean, LOG2)
#' @param cD A countData object.
#' @param groupings	A grouping (annotation column), e.g. groupings="something".
#' @param treatment1	Symbol, treatment 1.
#' @param treatment2	Symbol, treatment 2.
#' @param mode_mean 	Boolean, Calculate RowMeans or RowMedians.
#' @param LOG2	Boolean, Calculate LOG2.
#' @details This function completes summary statistics of the expression of the supplied countData object.
#' @return Returns an invisible list of summary statistics, kruskal test and raw data of a countData object, using ratios between selected treatments.
#' @author AJ Vaestermark, JR Walters.
#' @references The "doseR" package, 2018 (in press).

test_diffs <- function (cD, groupings= NULL, treatment1=NULL, treatment2=NULL, mode_mean=TRUE, LOG2=TRUE) {

  if(is.null(groupings)) {
    stop ('No groupings, e.g. groupings="something"...')
    return (NULL)
  }

  if(length(cD@RPKM) == 0) {
    stop ('No RPKM data saved in count data object... cancelling...')
    return (NULL)
  }

  if(is.null(treatment1) | is.null(treatment2) ) {
    stop ('Indicate treatments, such as  treatment1="A", treatment2="B"')
    return (NULL)
  }

  MyGroups<-cD@annotation[[groupings]]
  #require(matrixStats)

  RM<- (
    if(mode_mean) rowMeans(cD@RPKM[,cD@replicates==treatment1]) else matrixStats::rowMedians(cD@RPKM[,cD@replicates==treatment1])
  ) / (
    if(mode_mean) rowMeans(cD@RPKM[,cD@replicates==treatment2]) else matrixStats::rowMedians(cD@RPKM[,cD@replicates==treatment2])
  )

  if(LOG2) { RM<-log2(RM) }
  RM[is.infinite(RM)]<-NA

  tmp <-  split(RM, MyGroups)
  val.summary <-  sapply(tmp, summary)
  val.k <- kruskal.test(tmp)

  names(tmp) <- levels(as.factor(MyGroups))

  message("View output: outlist$kruskal, outlist$summary")
  invisible( list("summary" = val.summary, "kruskal" = val.k, "data" = tmp) )

}# test_diffs