Usage
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.