fixed bugs when .FUN = mt.rawp2adjp (31dfd2dd) · Commits · github_fork / LinkET

R/pvalue-adjust.R

+30 −4

Original line number	Diff line number	Diff line
		@@ -3,12 +3,18 @@
		#' @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 ... 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", ...) {
		adjust_pvalue <- function(x,
		.FUN = "p.adjust",
		method = "holm",
		proc = "Holm",
		...) {
		if (!inherits(x, "cor_md_tbl") && !inherits(x, "correlate")) {
		stop("Can only adjust p-value for 'md_tbl' and 'correlate' object.",
		call. = FALSE)
		@@ -17,11 +23,31 @@ adjust_pvalue <- function(x, .FUN = "p.adjust", ...) {
		return(x)
		}

		.FUN <- match.fun(.FUN)
		.FUN <- match.arg(.FUN, c("p.adjust", "mt.rawp2adjp"))

		if (.FUN == "p.adjust") {
		.FUN <- get_function("stats", "p.adjust")
		if (inherits(x, "cor_md_tbl")) {
		adj_p <- stats::p.adjust(x$p, method = method, n = nrows(x) * ncols(x))
		} else {
		adj_p <- stats::p.adjust(x$p, method = method)
		}
		} 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]
		}

		if (inherits(x, "cor_md_tbl")) {
		x$p <- .FUN(x$p, ...)
		x$p <- adj_p
		} else {
		x$p[] <- .FUN(x$p, ...)
		x$p[] <- adj_p
		}
		x
		}

man/adjust_pvalue.Rd

+5 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@
		\alias{adjust_pvalue}
		\title{Adjust p values}
		\usage{
		adjust_pvalue(x, .FUN = "p.adjust", ...)
		adjust_pvalue(x, .FUN = "p.adjust", method = "holm", proc = "Holm", ...)
		}
		\arguments{
		\item{x}{a correlate or md_tbl object.}
		@@ -12,6 +12,10 @@ adjust_pvalue(x, .FUN = "p.adjust", ...)
		\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{...}{other parameters passing on to adjust function.}
		}
		\value{

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