plotWordFreq: Plots word frequencies found within gene ontology terms

Description Usage Arguments Value Examples

Description

Creates barplots of word frequencies from gene ontology terms derived from either biological process (BP), cellular compartment (CC), or molecular function (MF) of genes-under-peaks that are unique between two different upstream extension levels.

Usage

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plotWordFreq(organism, start, end, GOcategory, GOspecies, word_count)

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).

word_count

Number of top words to display

Value

A barplot comprised of words sorted by frequency of occurrence from gene ontology terms of 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(tm)
library(SnowballC)
library(wordcloud)
library(RColorBrewer)
library(org.Rn.eg.db)
plotWordFreq(rat, 0, 500, BP, org.Rn.eg.db, 10)

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