getGO: Obtain gene ontology (GO) terms for given genes

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Obtain gene ontology (GO) terms for given genes

Description

Obtain gene ontology (GO) terms useing GO gene mapping package such as org.Hs.db.eg to obtain the GO annotation.

Usage

getGO(all.genes, orgAnn = "org.Hs.eg.db", writeTo, ID_type = "gene_symbol")

Arguments

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

Value

An invisible table with genes and GO terms.

Author(s)

Lihua Julie Zhu

See Also

getEnrichedGO

Examples

  if (interactive()) {
     data(annotatedPeak)
     library(org.Hs.eg.db)
     getGO(annotatedPeak[1:6]$feature, 
          orgAnn="org.Hs.eg.db", 
          ID_type="ensembl_gene_id")
}

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.