Match adjust function based on method (a1f42357) · Commits · github_fork / LinkET

R/pvalue-adjust.R

+10 −15

Original line number	Diff line number	Diff line
		#' @title Adjust p values
		#' @description Adjust correlation p values based on user-specified method.
		#' @param x a correlate or md_tbl object.
		#' @param .FUN adjust function, such as \code{stats::p.adjust()},
		#' \code{multtest::mt.rawp2adjp()}.
		#' @param method adjust method when .FUN is "p.adjust".
		#' @param proc adjust method when .FUN is "mt.rawp2adjp".
		#' @param method adjust method.
		#' @param ... other parameters passing on to adjust function.
		#' @return a object same as x.
		#' @author Hou Yun
		#' @rdname adjust_pvalue
		#' @export
		adjust_pvalue <- function(x,
		.FUN = "p.adjust",
		method = "holm",
		proc = "Holm",
		...) {
		adjust_pvalue <- function(x, method = "holm", ...) {
		if (!inherits(x, "cor_md_tbl") && !inherits(x, "correlate")) {
		stop("Can only adjust p-value for 'md_tbl' and 'correlate' object.",
		call. = FALSE)
		@@ -23,10 +16,14 @@ adjust_pvalue <- function(x,
		return(x)
		}

		.FUN <- match.arg(.FUN, c("p.adjust", "mt.rawp2adjp"))
		method <- match.arg(method, c("Bonferroni", "Holm", "Hochberg", "SidakSS",
		"SidakSD", "BH", "BY", "ABH", "TSBH", "holm",
		"hochberg", "hommel", "bonferroni", "fdr", "none"))
		if (method == "none") {
		return(x)
		}

		if (.FUN == "p.adjust") {
		.FUN <- get_function("stats", "p.adjust")
		if (method %in% stats::p.adjust.methods) {
		if (inherits(x, "cor_md_tbl")) {
		adj_p <- stats::p.adjust(x$p, method = method, n = nrows(x) * ncols(x))
		} else {
		@@ -34,14 +31,12 @@ adjust_pvalue <- function(x,
		}
		} else {
		.FUN <- get_function("multtest", "mt.rawp2adjp")
		proc <- match.arg(proc, c("Bonferroni", "Holm", "Hochberg", "SidakSS",
		"SidakSD", "BH", "BY", "ABH", "TSBH"))
		if (inherits(x, "cor_md_tbl")) {
		if (length(x$p) != nrows(x) * ncols(x)) {
		warning("Please adjust p-value before filter.", call. = FALSE)
		}
		}
		adj_p <- .FUN(rawp = x$p, proc = proc, ...)$adjp[, 2]
		adj_p <- .FUN(rawp = x$p, proc = method, ...)$adjp[, 2]
		}

		if (inherits(x, "cor_md_tbl")) {

man/adjust_pvalue.Rd

+2 −7

Original line number	Diff line number	Diff line
		@@ -4,17 +4,12 @@
		\alias{adjust_pvalue}
		\title{Adjust p values}
		\usage{
		adjust_pvalue(x, .FUN = "p.adjust", method = "holm", proc = "Holm", ...)
		adjust_pvalue(x, method = "holm", ...)
		}
		\arguments{
		\item{x}{a correlate or md_tbl object.}

		\item{.FUN}{adjust function, such as \code{stats::p.adjust()},
		\code{multtest::mt.rawp2adjp()}.}

		\item{method}{adjust method when .FUN is "p.adjust".}

		\item{proc}{adjust method when .FUN is "mt.rawp2adjp".}
		\item{method}{adjust method.}

		\item{...}{other parameters passing on to adjust function.}
		}

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