gdcEnrichAnalysis: Functional enrichment analysis

In Jialab-UCR/GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

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)

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.