epipathway: pathway annotation

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

Description

pathway identification significantly enriched by genes in one module.

Usage

epipathway(gene.list, cutoff = 0.05, prefix = NA, pdf.height = 10,
  pdf.width = 10)

Arguments

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.
cutoff	Cutoff value of qvalue for pathway enrichment
prefix	a prefix for PDF file name
pdf.height	An integer representing the height (in inches) of the outputted boxplot pdf file (default: 10)
pdf.width	An integer representing the width (in inches) of the outputted boxplot pdf file (default: 10)

Value

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,
                             prefix="CEBPA_sil",pdf.height = 10,
                             pdf.width = 10)

xiaowenchenjax/epihet documentation built on May 5, 2019, 9:20 a.m.