gdcEnrichAnalysis {GDCRNATools} | R Documentation

## Functional enrichment analysis

### Description

Performs Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Disease Ontology (DO) enrichment analyses by clusterProfiler and DOSE packages

### Usage

    gdcEnrichAnalysis(gene, simplify = TRUE, level = 0)

### Arguments

`gene` | a vector of Ensembl gene id
`simplify` | logical, specifying whether to remove redundant GO terms. Default `simplify=TRUE`
`level` | a numeric value, restrict the GO enrichment result at a specific GO level. Default is `0`, which means all terms should be returned

### Value

A dataframe of enrichment analysis result containing enriched terms, number of overlpped genes, p value of hypergeometric test, fdr, fold of enrichment, Ensembl gene ids, gene symbols, and functional categories, etc.

### Author(s)

Ruidong Li and Han Qu

### References

Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics: a journal of integrative biology. 2012 May 1;16(5):284-7.
Yu G, Wang LG, Yan GR, He QY. DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics. 2014 Oct 17;31(4):608-9.

### Examples

    ####### GO, KEGG, DO enrichment analysis #######
    deg <- c('ENSG00000000938','ENSG00000000971','ENSG00000001036',
            'ENSG00000001084','ENSG00000001167','ENSG00000001460')
    ## Not run: enrichOutput <- gdcEnrichAnalysis(gene=deg, simplify=TRUE)

[Package GDCRNATools version 1.14.0 Index]