obtain_enrich: obtain_enrich

View source: R/steps.R

obtain_enrichR Documentation

obtain_enrich

Description

Obtain enrichment analysis description

Usage

obtain_enrich(
  geneList,
  keyType = "SYMBOL",
  enrich = "kegg",
  org_db = org.Hs.eg.db,
  top_path = 30
)

Arguments

geneList

gene list

keyType

key type of gene list

enrich

'kegg' or 'reactome'

org_db

used to convert ID

top_path

the number of pathways to be obtained sorted by p-values

Details

The function performs enrichment analysis on queried vector, and returns the biotext object using the textual information from biological pathways.

Value

biotext class object

Examples

if (requireNamespace("clusterProfiler")) {
    testgenes <- c("IRF3","PNKP","DDX41","ERCC1","ERCC2","XRCC1")
    obtain_enrich(testgenes)
}

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.