R/dichotGSAR.R

In hui-sheen/MetaGSCA: Meta-analysis of Gene Set differential Co-expression Analysis

#' Dichotomize p-value matrix to 0-1 matrix for each PW across datasets��output metaP and metaFDR as well.
#'
#' @param input2PWcTalk File name of the CSV output file from prior metaGSAR analysis. This file includes k p-values for each pathway represented in rows (k: number of repetitive datasets). Several columns of meta-P values follow the dataset-specific p-value columns.
#' @param pTh.dataset cutoff value to dichotomize the continuous p-value from preceding MetaGSCA analysis. Low/significant p's are converted to 1's.  
dichotGSAR <- function(input2PWcTalk,pTh.dataset=0.01) {
  if (is.null(nrow(input2PWcTalk))) {# input is a file name, rather than the data frame
    input2PWcTalk <- read.csv(input2PWcTalk,as.is=TRUE,row.names=1)
  }
  metaGSAR <- input2PWcTalk
  GSAR <- metaGSAR[,-seq_along(c(1:3))]
  dichotP <- GSAR<=pTh.dataset
  dichotP[is.na(dichotP)] <- 0
  metaP <- metaGSAR[,'bootstrap.p']
  names(metaP) <- rownames(metaGSAR)
  res <- list(dichotP=dichotP,metaP=metaP)
}