R/module.extract.R

In DEComplexDisease: A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

#' Extract the patients and genes from module
#'
#' Return the patients and genes from module under user defined setting
#'
#' @docType methods
#'
#' @name module.exact
#' @param res.module a 'seed.module' or 'cluster.module' object returned by \code{\link{seed.module}} or \code{\link{cluster.module}}
#' @param mod a module name to extract genes and patients
#' @param n.patients the patient number to return
#' @param n.genes the gene number to return
#'
#' @author Guofeng Meng
#'
#'
#'
#' @details This function is used to return the patients and genes at user defined breakpoints.
#'
#' Users can set `n.patients` or `n.genes` to define the break points of bi-clustering. But it is not allowed to set both value.
#'
#' @return A list for genes or patients.
#'
#' @examples
#' # extract the genes and patients when 200 patients are observed in M1.
#' page=module.extract(cluster.mod, 'M1', n.patients=100)
#' head(page$patients)
#' head(page$geness)
#' # find genes and patients in patient-seeded module
#' module.extract(seed.mod, names(seed.mod)[1], n.patients=50)
#' @export

module.extract <- function(res.module, mod, n.patients = NULL, n.genes = NULL) {
    if (!is(res.module, "cluster.module") & !is(res.module, "seed.module") & !is(res.module, 
        "list")) 
        stop("Error: res.module: must the output of 'seed.module' or 'cluster.module'!")
    if (is.null(mod)) 
        stop("Error: mod: should be specified!")
    if (!mod %in% names(res.module)) 
        stop("Error: mod: cannot be recognized!")
    if (is.null(n.patients) & is.null(n.genes)) {
        return(list(genes = res.module[[mod]][["model"]][["genes"]], patients = res.module[[mod]][["model"]][["patients"]]))
    }
    n.pas = res.module[[mod]][["curve"]][["no.patient"]]
    n.ges = res.module[[mod]][["curve"]][["no.gene"]]
    if (!is.null(n.patients)) {
        wh = which.min(abs(n.pas - n.patients))
        n.patients = n.pas[wh]
        n.genes = n.ges[wh]
    }
    if (!is.null(n.genes)) {
        wh = which.min(abs(n.ges - n.genes))
        n.patients = n.pas[wh]
        n.genes = n.ges[wh]
    }
    seed = res.module[[mod]][["seed"]]
    seed.genes = names(seed[seed != 0])
    add.patients = res.module[[mod]][["patients.added"]]
    remove.genes = res.module[[mod]][["genes.removed"]]
    have.patients = add.patients[seq_len(n.patients)]
    have.genes = seed.genes[!seed.genes %in% remove.genes[seq_len(length(seed.genes) - 
        n.genes)]]
    return(list(genes = have.genes, patients = have.patients))
}