epiPathway: pathway annotation

Description Usage Arguments Value Examples

View source: R/epiPathway.R

Description

pathway identification significantly enriched by genes in one module.

Usage

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epiPathway(gene.list, cutoff = 0.05, showCategory = 8, 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 pvalue for pathway enrichment (default:0.05)

showCategory

number of categories to show (default:8)

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

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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)

epihet documentation built on Dec. 31, 2020, 2:01 a.m.