getGO {ChIPpeakAnno} | R Documentation |
Obtain gene ontology (GO) terms useing GO gene mapping package such as org.Hs.db.eg to obtain the GO annotation.
getGO(all.genes, orgAnn = "org.Hs.eg.db", writeTo, ID_type = "gene_symbol")
all.genes |
A character vector of feature IDs |
orgAnn |
Organism annotation package such as org.Hs.eg.db for human and org.Mm.eg.db for mouse, org.Dm.eg.db for fly, org.Rn.eg.db for rat, org.Sc.eg.db for yeast and org.Dr.eg.db for zebrafish |
writeTo |
File path for output table |
ID_type |
The feature type in annotatedPeak such as ensembl_gene_id, refseq_id, gene_symbol |
An invisible table with genes and GO terms.
Lihua Julie Zhu
getEnrichedGO
if (interactive()) { data(annotatedPeak) library(org.Hs.eg.db) getGO(annotatedPeak[1:6]$feature, orgAnn="org.Hs.eg.db", ID_type="ensembl_gene_id") }