R/adjustPVals.R

In DGCA: Differential Gene Correlation Analysis

#' @title Adjusts a numeric vector of p-values.
#' @description Wraps around the R base implementation of p.adjust, as well as the methods used in the fdr tool package.
#' @param pVals Numeric vector of p-values to adjust.
#' @param adjust Allows for resulting p-values to be corrected for multiple hypothesis tests. Optional and some non-default choices require the "fdrtool" package. Default = "none", which means that no p-value adjustment is performed. Other options include methods in ?p.adjust (i.e., "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"), and methods in ?fdrtool (i.e., "fndr", "pct0", "locfdr").
#' @param plotFdr Allows for plotting of fdrtool p-value adjustment result, if this is chosen. Requires fdrtool package. Default = FALSE.
#' @param verbose If TRUE, the function prints out the general method used for multiple correction analysis. Default = FALSE.
#' @return A numeric vector of p-values that have been adjusted according to the specified method.
#' @examples
#' pvals = runif(100, 0, 1)
#' adj_pvals_bh = adjustPVals(pvals, adjust = "BH")
#' adj_pvals_hommel = adjustPVals(pvals, adjust = "hommel")
#' @export
adjustPVals <- function(pVals, adjust = "none", plotFdr = FALSE,
	verbose = FALSE){

	p_adjust_methods = c("holm", "hochberg", "hommel", "bonferroni", "BH",
		"BY", "fdr")
	fdrtool_methods = c("fndr", "pct0", "locfdr")

	if(!(adjust %in% c("none", p_adjust_methods, fdrtool_methods))){
		stop("Adjust method is one of the available methods.")
	}

	pVals = as.numeric(pVals)

	if(adjust == "none"){
		if(verbose){
			message("No adjustment of p-values for multiple comparisons.")
		}
		pvals_adj = pVals
	}

	if(adjust %in% p_adjust_methods){
		if(verbose){
			message(paste0("Adjusting p-values for multiple comparisons using ", adjust, " method in p.adjust."))
		}
		pvals_adj = p.adjust(pVals, method = adjust)
	}

	if(adjust %in% fdrtool_methods){
		if (!requireNamespace("fdrtool", quietly = TRUE)) {
			stop("fdrtool is needed for the p-value adjustment technique you chose to work. Please install it.",
				call. = FALSE)
		}
		if(verbose){
			message("Adjusting p-vals for multiple comparisons using fdrtool, and selecting the local FDR result.")
		}
		pvals_adj = suppressMessages(fdrtool::fdrtool(pVals,
			statistic = "pvalue", plot = plotFdr, cutoff.method = adjust, verbose = verbose))
		pvals_adj = pvals_adj$lfdr
	}

	return(pvals_adj)

}