gcap.enrich: Enrichment Analysis

In ShixiangWang/gcaputils: Utils for Package 'gcap'

Enrichment Analysis

Description

Enrichment Analysis

Usage

gcap.enrich(
  geneList,
  analysis_func = c("enricher", "fgsea"),
  gene_encode = c("ensembl", "symbol"),
  species = "Homo sapiens",
  category = "H",
  subcategory = "",
  genome_build = c("hg38", "hg19"),
  ...
)

Arguments

geneList	a vector (list) of genes. If the vector is named, the names must be genes and values must numeric.
analysis_func	analysis function to run.
gene_encode	gene ID type from input.
species	species, not to change.
category	gene set main category name.
subcategory	gene set sub-category name.
genome_build	genome version.
...	other parameters passing to clusterProfiler::enricher() or fgsea::fgsea.

Value

depends on data and analysis_func.

Examples

if (require("clusterProfiler")) {
  gcap.enrich(c("TP53", "MYC", "ABC", "EGFR", "GSX2"), gene_encode = "symbol")
}

if (require("fgsea")) {
  gcap.enrich(c("TP53", "MYC", "ABC", "EGFR", "GSX2"),
    gene_encode = "symbol", analysis_func = "fgsea"
  )
}

ShixiangWang/gcaputils documentation built on Feb. 14, 2023, 5:58 a.m.