Package `clusterProfiler`

Package ‘clusterProfiler’ February 9, 2015 Type Package Title statistical analysis and visulization of functional profiles for genes and gene clusters Version 2.0.0 Author Guangchuang Yu, Li-Gen Wang Maintainer Guangchuang Yu Description This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters. Depends R (>= 3.0.0) Imports methods, stats4, plyr, ggplot2, AnnotationDbi, GO.db, KEGG.db, DOSE, GOSemSim Suggests org.Hs.eg.db, ReactomePA, pathview, knitr VignetteBuilder knitr License Artistic-2.0 URL https://github.com/GuangchuangYu/clusterProfiler biocViews Clustering, GO, Pathways, Visualization, MultipleComparison, GeneSetEnrichment

R topics documented: clusterProfiler-package . . . buildGOmap . . . . . . . . cnetplot . . . . . . . . . . . compareCluster . . . . . . . compareClusterResult-class . DataSet . . . . . . . . . . . enrichGO . . . . . . . . . . enrichKEGG . . . . . . . . enrichMap . . . . . . . . . . getGeneSet.BP . . . . . . . getGeneSet.CC . . . . . . .

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clusterProfiler-package getGeneSet.GO . . . getGeneSet.KEGG . getGeneSet.MF . . . getGOLevel . . . . . Gff2GeneTable . . . groupGO . . . . . . groupGOResult-class gseaplot . . . . . . . gseGO . . . . . . . . gseKEGG . . . . . . plot . . . . . . . . . plotting.clusterProfile viewKEGG . . . . .

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Index

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clusterProfiler-package statistical analysis and visulization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.

Description This package is designed to compare gene clusters functional profiles. Details Package: Type: Version: Date: biocViews: Depends: Suggests: License:

clusterProfiler Package 1.9. 06-13-2013 GO, Clustering, Visulization AnnotationDbi, GO.db, org.Hs.eg.db, ggplot2, plyr, methods GOSemSim Artistic-2.0

Author(s) Guangchuang Yu Maintainer: Guangchuang Yu

buildGOmap

3

See Also compareClusterResult, groupGOResult enrichResult

buildGOmap

buildGOmap

Description building GO mapping files Usage buildGOmap(gomap, compress = TRUE) Arguments gomap

data.frame with two columns names "entrezgene", and "go_accession"

compress

logical, indicate file save in compress or not.

Details provided by a data.frame of gene and GO directly annotation file this function will building gene to GO and GO to gene mapping, with directly and undirectly annotation. Value files save in the the working directory Author(s) Yu Guangchuang

cnetplot

Description category-gene-net plot Usage cnetplot(x, ...)

cnetplot

4

compareCluster

Arguments x

enrichResult object

...

additional parameter

Details category gene association Value figure Author(s) ygc

compareCluster

Compare gene clusters functional profile Given a list of gene set, this function will compute profiles of each gene cluster.

Description Compare gene clusters functional profile Given a list of gene set, this function will compute profiles of each gene cluster. Usage compareCluster(geneClusters, fun = "enrichGO", ...) Arguments geneClusters

a list of entrez gene id.

fun

One of "groupGO", "enrichGO", "enrichKEGG", "enrichDO" or "enrichPathway" .

...

Other arguments.

Value A clusterProfResult instance. Author(s) Guangchuang Yu http://ygc.name See Also compareClusterResult-class, groupGO enrichGO

compareClusterResult-class

5

Examples data(gcSample) xx