R/P_null.R

In pageRank: Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

#' Build Null Distribution of Probability-Based Distance
#'
#' Build null model for evaluating the significance of interactions by
#' generating random regulator-target pairs.
#'
#' @param expmat (matrix) Gene expression matrix.
#'
#' @param net (data.frame) Network, with "reg" and "target" in column name.
#'
#' @param n (numeric) Number of random pairs.
#'
#' @param sep (numeric) Number of bins for calculating marginal/joint
#' probability.
#'
#' @param method (character) Method for calculating probability-based distance,
#' either PXY-PXPY ("difference") or mutual information ("mi").
#'
#' @return (ecdf) ECDF of null distribution.
#'
#' @examples
#' library(bcellViper)
#' data(bcellViper)
#' dset <- exprs(dset)
#' net <- do.call(rbind, lapply(1:10, function(i, regulon){
#'   data.frame(reg=rep(names(regulon)[i], 10),
#'              target=names(regulon[[i]][[1]])[1:10],
#'              direction=rep(1, 10),
#'              stringsAsFactors = FALSE)}, regulon=regulon))
#' P_null(dset, net, n=100, method="difference")
#'
#' @author DING, HONGXU (hd2326@columbia.edu)
#'
#' @importFrom stats ecdf
#'
#' @export

P_null <- function(expmat, net, n=10000, sep=5, method=c("difference", "mi")){
    net <- data.frame(reg=sample(unique(net$reg), size=n, replace=TRUE),
                      target=sample(unique(net$target), size=n, replace=TRUE),
                      stringsAsFactors=FALSE)
    bin <- gene_bin(genes=union(net$reg, net$target), expmat=expmat, sep=sep)
    px <- PX(expmat=expmat, bin=bin)
    pxy <- PXY(expmat=expmat, bin=bin, x=net$reg, y=net$target)
    pxpy <- PXPY(px=px, combinations=names(pxy))
    dist <- P_dist(pxy=pxy, pxpy=pxpy, method=method)
    null <- ecdf(unlist(dist))
    return(null)}