GOSlimSummary: Summary the gene list based on the GO (Gene Ontology) Slim...

Description Usage Arguments Value Note Author(s) Examples

View source: R/GOSlimSummary.R

Description

This function can summary the gene list based on the biological process, cellular component and molecular function ontologies of the GO Slim data sets. The summary result will be plotted as three bar plots and outputted to the PDF file.

Usage

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GOSlimSummary(organism, genelist, outputFile, outputType, hostName)

Arguments

organism

Currently, GOSlimSummary supports 12 organisms. Users can use the function listOrganism to check the available organisms.

genelist

An R vector object containing a gene list. GOSlimSummary only supports NCBI EntrezGene ID for the summary. For other ID types, please first use IDMapping function to map to the EntrezGene ID.

outputFile

The output file name.

outputType

The output file extension that can be pdf, png, or bmp.

hostName

The server URL for accessing the data. User can use listArchiveURL function to get all archive version URL.

Value

GOSlimSummary function will return a high-resolution image containing the summary information of the uploaded gene list based on the biological process (red bar plot), cellular component (blue bar plot) and molecular function (green bar plot) ontologies.

Note

Because the GOSlimSummary function will read the GO Slim data from the server, the running time for this function will be also based on the internet speed. Generally, it will take around 20 seconds to perform the summary analysis.

Author(s)

Jing Wang

Examples

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geneFile<-system.file("extdata","GOSlimExample.txt",package="WebGestaltR")
geneList<-read.table(geneFile,header=FALSE,sep="\t",stringsAsFactors=FALSE)
geneList<-as.vector(as.matrix(geneList))
outputFile<-paste(getwd(),"/GOSlimSummary",sep="")
#GOSlimSummary(organism="hsapiens", genelist=geneList, 
#outputFile=outputFile, outputType="pdf")

WebGestaltR documentation built on May 30, 2017, 8:17 a.m.