epiPathway {epihet} | R Documentation |
pathway identification significantly enriched by genes in one module.
epiPathway(gene.list, cutoff = 0.05, showCategory = 8, prefix = NA, pdf.height = 10, pdf.width = 10)
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) |
a data frame containing pathways that are significantly enriched by genes from one module
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)