By R on G. Yu
clusterProfiler supports over-representation test and gene set
enrichment analysis of Gene Ontology. It supports GO annotation from
OrgDb object, GMT file and user’s own data.
support many species
In github version of clusterProfiler, enrichGO and gseGO functions
removed the parameter organism and add another parameter OrgDb, so
that any species that have OrgDb object available can be analyzed in
clusterProfiler. Bioconductor have already provide OrgDb for about
20 species, see
http://bioconductor.org/packages/release/BiocViews.html#___OrgDb, and
users can build OrgDb via AnnotationHub.
library(AnnotationHub)
hub support many ID types
The input ID type can be any type that was supported in OrgDb object.
library(org.Hs.eg.db)
data(geneList)
gene 2]
gene.df Using SYMBOL directly is not recommended. User can use setReadable
function to translate geneID to gene symbol.
ego enrichGO test the whole GO corpus and enriched result may contains
very general terms. User can use dropGO function to remove specific GO
terms or GO level. If user want to restrict the result at sepcific GO
level, they can use gofilter function. We also provide a simplify
method to reduce redundancy of enriched GO terms, see the
post.
Visualization functions
dotplot(ego, showCategory=30)
enrichMap(ego, vertex.label.cex=1.2, layout=igraph::layout.kamada.kawai)
cnetplot(ego, foldChange=geneList)
plotGOgraph(ego)
##
## groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
##
## Building most specific GOs ..... ( 335 GO terms found. )
##
## Build GO DAG topology .......... ( 335 GO terms and 667 relations. )
##
## Annotating nodes ............... ( 11632 genes annotated to the GO terms. )
## $dag
## A graphNEL graph with directed edges
## Number of Nodes = 29
## Number of Edges = 50
##
## $complete.dag
## [1] "A graph with 29 nodes."
Gene Set Enrichment Analysis
gsecc 
GO analysis using user’s own data
clusterProfiler provides enricher function for hypergeometric test and
GSEA function for gene set enrichment analysis that are designed to
accept user defined annotation. They accept two additional parameters
TERM2GENE and TERM2NAME. As indicated in the parameter names, TERM2GENE
is a data.frame with first column of term ID and second column …read more
Source:: r-bloggers.com
