#' Rank products of a matrix where larger statistics have stronger rank
#'
#' Rank products of a matrix. Larger statistics have stronger rank.
#'
#' @param mat Numeric matrix with columns holding statistics per comparison & rows are analytes.
#' @param nsim Numeric number of simulations.
#' @param seed Random seed.
#' @inheritParams ezlimma::ezcor
#' @return Data frame with statistics from rank products test.
#' @export
rankprod <- function(mat, nsim=1e7-2, reorder.rows=TRUE, prefix=NULL, seed=100){
stopifnot(!is.null(colnames(mat)))
if(nsim > 1e7-2) stop("nsim too large to have enough precision")
rmat <- apply(mat, 2, rank)
rmat <- rmat/nrow(mat)
colnames(rmat) <- paste(gsub("\\..$", "", colnames(mat)), "Rank.Prop", sep=".")
set.seed(seed)
# last argument nsim is for anonymous function
rmat.sim <- apply(rmat, 2, function(v, nsim) sample(v, size=nsim, replace=TRUE), nsim)
# make stats negative, since using lower-tail for testing
rankprod <- -1 * apply(rmat, 1, prod)
rankprod.sim <- -1 * apply(rmat.sim, 1, prod)
Fn <- stats::ecdf(c(rankprod.sim, Inf, -Inf))
pval <- Fn(rankprod)
fdr <- stats::p.adjust(pval, method="BH")
res <- data.frame(rmat, Rankprod.p=pval, Rankprod.FDR=fdr, row.names=rownames(mat))
if(reorder.rows) res <- res[order(res$Rankprod.p), ]
if(!is.null(prefix)) colnames(res) <- paste(prefix, colnames(res), sep=".")
return(res)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.