R/gene_bin.R

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

#' Bin Gene Expression Space
#'
#' Bin gene expression space for marginal/joint probability calculation.
#'
#' @param genes (character) Genes to be analyzed.
#'
#' @param expmat (matrix) Gene expression matrix.
#'
#' @param sep (numeric) Number of bins.
#'
#' @return (matrix) Border values of gene expression bins.
#'
#' @author DING, HONGXU (hd2326@columbia.edu)
#' 
#' @keywords internal

gene_bin <- function(genes, expmat, sep=5){
    expmat <- expmat[intersect(genes, rownames(expmat)), ]
    table <- t(apply(expmat, 1, function(x, sep){
        seq(min(x), max(x), length.out = (sep+1))}, sep=sep))
    colnames(table) <- paste("bin", seq_len(sep+1), sep = "_")
    return(table)}