diffGO: Finds differential gene ontologies

In Bohdan-Khomtchouk/geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

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)

Bohdan-Khomtchouk/geneXtendeR documentation built on June 9, 2019, 2:53 a.m.