R/filter.cpm.R

In jhart99/gseasier: Run the GSEA java pacakage from inside R

# Copyright ---------------------------------------------------------------
# 2014 The Scripps Research Institute Author: Jonathan Ross Hart

# Author ------------------------------------------------------------------
# Jonathan Ross Hart(jonathan@jonathanrosshart.com)

# Description -------------------------------------------------------------
# Filter a gct object for genes with low expression

# Input -------------------------------------------------------------------
# Gene expression data and genesets

# Methods -------------------------------------------------

# Outputs -------------------------------------------------


# Library imports ---------------------------------------------------------



#' Title
#'
#' @param gct
#' @param cls
#' @param min.cpm
#' @param contrast
#'
#' @return
#' @export
#'
#' @examples
filter.cpm <- function(gct, cls, min.cpm = 1, contrast = NULL) {
  if (is.null(contrast)) {
    contrast <- list(levels(cls)[1], levels(cls)[2])
  }
  len1 <- sum(cls %in% contrast[[1]])
  len2 <- sum(cls %in% contrast[[2]])
  selection1 <- rowSums(gct[, which(cls %in% contrast[[1]]) + 2] > min.cpm)
  selection2 <- rowSums(gct[, which(cls %in% contrast[[2]]) + 2] > min.cpm)
  gct[(selection1 == len1) & (selection2 == len2), ]
}