functionEnrich {eegc} | R Documentation

## Funtional Enrichment Analysis

### Description

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

### Usage

    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

    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)

[Package eegc version 1.12.0 Index]