Functions to generate species-specific CMAPCollections from Bioconductor KEGG.db, reactome.db or GO.db annotation packages or the wikipathways http://www.wikipathways.org/index.php/Download_Pathways project.

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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

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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.

Note

The reactome.db package is currently broken. Unfortunately, the reactome2cmap function is defunct until the annotation package has been fixed.

Author(s)

Thomas Sandmann

See Also

induceCMAPCollection

Examples

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## 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)

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