makeNetwork: Makes gene-GO networks

Description Usage Arguments Value Examples

Description

Creates dynamic and interactive networks of genes linked to their respective 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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makeNetwork(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

An interactive network of gene names linked to their respective gene ontology terms for either a BP, CC, or MF category.

Examples

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library(rtracklayer)
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)
library(networkD3)
library(dplyr)
library(org.Rn.eg.db)
makeNetwork(rat, 0, 500, BP, org.Rn.eg.db)

Bohdan-Khomtchouk/geneXtendeR_keepme documentation built on June 3, 2019, 10:09 p.m.