gdcEnrichAnalysis {GDCRNATools} | R Documentation |
Performs Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Disease Ontology (DO) enrichment analyses by clusterProfiler and DOSE packages
gdcEnrichAnalysis(gene, simplify = TRUE, level = 0)
gene |
a vector of Ensembl gene id |
simplify |
logical, specifying whether to remove redundant GO terms.
Default |
level |
a numeric value, restrict the GO enrichment result at a
specific GO level. Default is |
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.
Ruidong Li and Han Qu
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.
####### GO, KEGG, DO enrichment analysis ####### deg <- c('ENSG00000000938','ENSG00000000971','ENSG00000001036', 'ENSG00000001084','ENSG00000001167','ENSG00000001460') ## Not run: enrichOutput <- gdcEnrichAnalysis(gene=deg, simplify=TRUE)