R/getGenePathways.R

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

#' Map features (genes) to feature list (genesets)
#'
#' This function will create a named vector of collapsed names of named
#' genesets list, separated by '; '
#' @param genesets A named list of features in row names of dataMatrix.
#' @keywords clustering
#' @return A named vector
#' @export
#' @examples
#' ## Read in ExpressionSet object
#' library(Biobase)
#' data(sample.ExpressionSet)
#'
#' ## Create dummy set of gene sets
#' genes <- rownames(sample.ExpressionSet)
#' genesetsMadeUp <- list(
#'     GS1=genes[1:50],
#'     GS2=genes[51:100],
#'     GS3=genes[101:150])
#'
#' head(getGenePathways(genesetsMadeUp))
#'

getGenePathways <- function(genesets) {

    ## Get unique gene and geneset ids
    geneNames <- unique(unlist(genesets))
    genesetNames <- names(genesets)

    genesetMat <- do.call(cbind, lapply(genesets, function(x) geneNames %in%
        x))

    ## Get set of pathways in which each gene resides
    gene2Pathway <- apply(genesetMat, 1, function(x) paste(genesetNames[x],
        collapse="; "))
    names(gene2Pathway) <- geneNames

    return(gene2Pathway)
}