functionEnrich: Funtional Enrichment Analysis

Description Usage Arguments Value Examples

View source: R/functionEnrich.R

Description

This function performs Gene Ontology (GO) and KEGG pathways functional enrichment for the five gene categories by calling clusterProfiler package.

Usage

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functionEnrich(cate.gene, organism = "human", convert = TRUE, from = "SYMBOL", ont = "BP",
pAdjustMethod = "bonferroni", GO = TRUE, KEGG = FALSE, enrichResult = FALSE)

Arguments

cate.gene

a list of the five gene categories, alternatively output by categorizeGene.

organism

a character of organism "human" or "mouse" to indicate the species of background genes.

convert

logical to determine whether the gene ID should be converted to "ENTREZID", default to TRUE.

from

the gene id type of input data, see the key types of org.Hs.eg.db.

ont

One of "MF", "BP", and "CC" subontologies, see enrichGO.

pAdjustMethod

correction method for p-value, one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none", default to "fdr", see details in p.adjust.

GO

logical to determine whether the functional enrichment is performed on Gene Ontology, default to TRUE.

KEGG

logical to determine whether the functional enrichment is performed on KEGG pathways, default to FALSE.

enrichResult

logical to determine if the "enrichResult" is output, default to FALSE to output a summary of the "enrichResult".

Value

Function enrichment analysis results.

Examples

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data(cate.gene)
# result in "enrichResult" class by specifying TRUE to enrichResult parameter
goenrichraw = functionEnrich(cate.gene, organism = "human", pAdjustMethod = "fdr",
                             GO = TRUE, KEGG = FALSE, enrichResult = TRUE)

# result of the summary of "enrichResult" by specifying FALSE to enrichResult parameter
# GO enrichment
goenrich = functionEnrich(cate.gene, organism = "human", pAdjustMethod = "fdr",
                          GO = TRUE, KEGG = FALSE, enrichResult = FALSE)

# KEGG enrichment
keggenrich = functionEnrich(cate.gene, organism = "human", pAdjustMethod = "fdr",
                            GO = FALSE, KEGG = TRUE, enrichResult = FALSE)

eegc documentation built on May 31, 2017, 11:41 a.m.