diffGO: Finds differential gene ontologies

Description Usage Arguments Value Examples

View source: R/diffGO.R

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

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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

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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)

geneXtendeR documentation built on Nov. 1, 2018, 3:34 a.m.