diffGO {geneXtendeR} | R Documentation

## Finds differential gene ontologies

### Description

Determines gene ontology terms for each category (biological process (BP), cellular compartment (CC), molecular function (MF)) of genes-under-peaks that are unique between two different upstream extension levels.

### Usage

    diffGO(organism, start, end, GOcategory, GOspecies)

### Arguments

`organism` | Object name assigned from readGFF() command.
`start` | Lower bound of upstream extension.
`end` | Upper bound of upstream extension.
`GOcategory` | Either BP, CC, or MF.
`GOspecies` | Either org.Ag.eg.db (mosquito), org.Bt.eg.db (bovine), org.Ce.eg.db (worm), org.Cf.eg.db (canine), org.Dm.eg.db (fly), org.Dr.eg.db (zebrafish), org.Gg.eg.db (chicken), org.Hs.eg.db (human), org.Mm.eg.db (mouse), org.Mmu.eg.db (rhesus), org.Pt.eg.db (chimpanzee), org.Rn.eg.db (rat), org.Sc.sgd.db (yeast), org.Ss.eg.db (pig), or org.Xl.eg.db (frog).

### Value

A data frame of gene symbol, gene ontology ID, and gene ontology term for either a BP, CC, or MF category. This data frame displays the annotations of all unique genes (i.e., genes that are located under peaks between two upstream extension levels) with their respective gene ontology information.

### Examples

    library(rtracklayer)
    library(org.Rn.eg.db)
    rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
    fpath <- system.file("extdata", "somepeaksfile.txt", package="geneXtendeR")
    peaksInput(fpath)
    diffGO(rat, 0, 500, BP, org.Rn.eg.db)

[Package geneXtendeR version 1.16.0 Index]