geneListPie: Profiling a gene list into GOslim or KEGG function pie
Version 1.0

"geneListPie" package is for mapping a gene list to function categories defined in GOSlim or Kegg. The results can be plotted as a pie chart to provide a quick view of the genes distribution of the gene list among the function categories. The gene list must contain a list of gene symbols. The package contains a set of pre-processed gene sets obtained from Gene Ontology and MSigDB including human, mouse, rat and yeast. To provide a high level concise view, only GO slim and kegg are provided. The gene sets are regulared updated. User can also use customized gene sets. User can use the R Pie() or Pie3D() function for plotting the pie chart. Users can also choose to output the gene function mapping results and use external software such as Excel(R) for ploting.

Browse man pages Browse package API and functions Browse package files

AuthorXutao Deng
Date of publication2012-07-23 10:35:32
MaintainerXutao Deng <xutaodeng@gmail.com>
LicenseGPL-3
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("geneListPie")

Man pages

geneListPie-package: Profiling a gene list into GOslim or KEGG function pie
geneListProfile: Profling a gene list against gene sets
goslim.human.all: goslim.human.all
goslim.human.BP: goslim.human.BP
goslim.human.CC: goslim.human.CC
goslim.human.MF: goslim.human.MF
goslim.mouse.all: goslim.mouse.all
goslim.mouse.BP: goslim.mouse.BP
goslim.mouse.CC: goslim.mouse.CC
goslim.mouse.MF: goslim.mouse.MF
goslim.rat.all: goslim.rat.all
goslim.rat.BP: goslim.rat.BP
goslim.rat.CC: goslim.rat.CC
goslim.rat.MF: goslim.rat.MF
goslim.yeast.all: goslim.yeast.all
goslim.yeast.BP: goslim.yeast.BP
goslim.yeast.CC: goslim.yeast.CC
goslim.yeast.MF: goslim.yeast.MF
kegg2.5.generic: kegg2.5.generic
load.genelist: load a gene list into workspace
load.genesets: Load customized gene sets into work space
printGeneListProfile: Print the profiling results

Functions

geneListPie Man page
geneListPie-package Man page
geneListProfile Man page Source code
goslim.human.BP Man page
goslim.human.CC Man page
goslim.human.MF Man page
goslim.human.all Man page
goslim.mouse.BP Man page
goslim.mouse.CC Man page
goslim.mouse.MF Man page
goslim.mouse.all Man page
goslim.rat.BP Man page
goslim.rat.CC Man page
goslim.rat.MF Man page
goslim.rat.all Man page
goslim.yeast.BP Man page
goslim.yeast.CC Man page
goslim.yeast.MF Man page
goslim.yeast.all Man page
kegg2.5.generic Man page
load.genelist Man page Source code
load.genesets Man page Source code
printGeneListProfile Man page Source code

Files

MD5
R
R/geneListPie.R
man
man/goslim.rat.BP.Rd
man/goslim.mouse.BP.Rd
man/goslim.human.all.Rd
man/geneListProfile.Rd
man/goslim.mouse.all.Rd
man/load.genesets.Rd
man/kegg2.5.generic.Rd
man/goslim.mouse.MF.Rd
man/goslim.yeast.BP.Rd
man/printGeneListProfile.Rd
man/goslim.human.CC.Rd
man/goslim.yeast.MF.Rd
man/goslim.rat.CC.Rd
man/goslim.rat.all.Rd
man/goslim.yeast.all.Rd
man/geneListPie-package.Rd
man/load.genelist.Rd
man/goslim.mouse.CC.Rd
man/goslim.human.BP.Rd
man/goslim.rat.MF.Rd
man/goslim.human.MF.Rd
man/goslim.yeast.CC.Rd
NAMESPACE
DESCRIPTION
data
data/goslim.mouse.all.RData
data/kegg2.5.generic.RData
data/goslim.rat.BP.RData
data/goslim.yeast.BP.RData
data/goslim.rat.all.RData
data/goslim.mouse.MF.RData
data/goslim.human.BP.RData
data/goslim.mouse.CC.RData
data/goslim.human.CC.RData
data/goslim.yeast.all.RData
data/goslim.yeast.CC.RData
data/goslim.human.all.RData
data/goslim.human.MF.RData
data/goslim.mouse.BP.RData
data/datalist
data/goslim.rat.MF.RData
data/goslim.rat.CC.RData
data/goslim.yeast.MF.RData
geneListPie documentation built on May 19, 2017, 5:32 p.m.