plotWordFreq: Plots word frequencies found within gene ontology terms

In geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

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

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

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)

geneXtendeR documentation built on Nov. 8, 2020, 11:09 p.m.