R/epiPathway.R

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

#' @title  pathway annotation
#' @description pathway identification significantly enriched by genes
#' in one module.
#' @param gene.list a data frame generated from network.construct() function.
#' The first column is gene entrez ID, the second column is module lable,
#' the third column is module color
#' @param cutoff Cutoff value of pvalue for pathway enrichment (default:0.05)
#' @param prefix a prefix for PDF file name
#' @param pdf.height An integer representing the height (in inches)
#' of the outputted boxplot pdf file (default: 10)
#' @param pdf.width An integer representing the width (in inches) of
#' the outputted boxplot pdf file (default: 10)
#' @return a data frame containing pathways that are significantly enriched
#' by genes from one module
#' @examples
#' genelist<-data.frame(ENTREZID=c("2902","2905","3360","286223","59338",
#' "344018","5144","55001","7410","730051","55743","6804","200634","2802",
#' "2260","651","2104","23432","10505","23194","9855","7101",
#' "389136","124857","1829","3164","3754","8614","9469","3217","9578",
#' "10516","10630"),label=rep(18,33),color=rep("lightgreen",33),
#' stringsAsFactors = FALSE)
#' pathway <- epihet::epiPathway(genelist,cutoff = 0.05,showCategory = 2,
#'                              prefix="CEBPA_sil",pdf.height = 10,
#'                              pdf.width = 10)
#' @export
epiPathway <- function(gene.list, cutoff = 0.05, showCategory = 8, prefix = NA,
    pdf.height = 10, pdf.width = 10) {
    module.id <- unique(gene.list[, 3])
    pathway.result <- list()
    for (i in module.id) {
        print(i)
        dat <- gene.list[which(gene.list[, 3] == i), 1]
        x <- ReactomePA::enrichPathway(gene = dat, pvalueCutoff = cutoff,
            readable = TRUE)
        sigPathNum <- length(which(x@result$p.adjust < cutoff))
        if (sigPathNum == 0) {
            print(paste("Could not find significantly enriched pathways for",
                paste("ME", i, sep = "")), sep = " ")

        } else {
            barplot(x, showCategory = showCategory)
            ggsave(paste(prefix, i, "pathway.pdf", sep = "_"),
                height = pdf.height, width = pdf.width)
            pathway.result[[paste("ME", i, sep = "")]] = x
        }
    }
    return(pathway.result)
}