KEGG2cmap: Functions to generate species-specific CMAPCollections from...

Description Usage Arguments Value Author(s) See Also Examples

Description

These functions extract the gene sets defined for a species of interest from the KEGG, Reactome or GO annotation packages or download the latest gene sets from the Wikipathways website and create a CMAPCollections. Wikipathways provides gene identifiers using different annotation sources; the wiki2cmap function only considers Entrez and Ensembl gene identifiers and return a CMAPCollection with Entrez ids. Please note that the GO graph structure will be used to associate every gene with all upstream annotation terms. The relationships between GO categories is not represented in the output CMAPCollection.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
KEGG2cmap(species,
          annotation.package,
          min.size=5,
          max.size=200)
reactome2cmap(species,
              annotation.package,
              min.size=5,
              max.size=200)
wiki2cmap(species,
          annotation.package,
          min.size=5,
          max.size=200 )
go2cmap(annotation.package="org.Hs.eg.db",
        ontology="BP",
        evidence=NULL,
        min.size=5,
        max.size=200)

Arguments

species

Character, the identifier used by the KEGG or Reactome databases to identify the species of interest. For example, human categories are identified by 'Homo sapiens' in the Reactome and 'hsa' in the KEGG database.

annotation.package

Character, the name of the Bioconductor annotation package for the species of interest, e.g. 'org.Hs.eg.db' for human gene annotations.

ontology

One of 'BP', 'MF' and 'CC', identifying the 'biological process', 'molecular function' and 'cellular component' gene ontology domain of interest.

evidence

Character string identifying the evidence required for a GO annotation to be included in the result. If 'NULL' all annotated terms will be included.

min.size

Scalar integer, only gene sets with at least 'min.size' members will be returned.

max.size

Scalar integer, only gene sets with no more than 'max.size' members will be returned.

Value

A CMAPCollection object.

Author(s)

Thomas Sandmann

See Also

induceCMAPCollection

Examples

1
2
3
4
5
6
7
8
9
## Not run: 
KEGG2.hs <- KEGG2cmap( species="hsa",
                       annotation.package="org.Hs.eg.db")
#reactome.hs <- reactome2cmap( species="Homo sapiens",
#                              annotation.package="org.Hs.eg.db")
wikipathways.hs <- wiki2cmap( species="Homo sapiens",
                              annotation.package="org.Hs.eg.db")

## End(Not run)


Search within the gCMAP package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.