makeNetwork {geneXtendeR} | R Documentation

## Makes gene-GO networks

### 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

    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

    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)

[Package geneXtendeR version 1.12.0 Index]