R/KW_test.R

In satabdisaha1288/scBT: What the Package Does (One Line, Title Case)

#' Performs a genewise Kruskal Wallis test on a SingleCellExperiment object
#'
#' @author Jack Dodson
#' @param sce SingleCellExperiment object with a logcounts assay
#' and Dose column in the cell metadata
#'
#' @return a vector of p values from the Kruskal Wallis test
#' @export
batchKW <- function(sce){
  data <- as.matrix(logcounts(sce))
  dose <- colData(sce)[,"Dose"]
  kw.pvalues <- apply(data, 1, function(x) runKW(x, dose))
  kw.out <- data.frame(kw.pvalues)
  kw.out$adjusted.p <- p.adjust(kw.out$kw.pvalues, 'fdr')
  kw.out[which(is.nan(kw.out$adjusted.p)), 'adjusted.p'] <- 1
  return(kw.out)
}

#' Performs a Kruskal Wallis test on a logcounts vactor for a given dose
#'
#' @author Jack Dodson
#' @param data The logcounts vector
#' @param dose The dose to analyze
#'
#' @return A p value from the Kruskal Wallis test
#' @export
runKW <- function(data, dose){
  my_data <- data.frame(value = data, dose = dose)
  res.kw <- kruskal.test(data ~ dose, data = my_data)
  kw.pvalue <- res.kw[[3]]
  return(kw.pvalue)
}