| org.Hs.egPATH {org.Hs.eg.db} | R Documentation |
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. org.Hs.egPATH maps entrez gene identifiers to the identifiers used by KEGG for pathways
Each KEGG pathway has a name and identifier. Pathway name for a given pathway identifier can be obtained using the KEGG data package that can either be built using AnnBuilder or downloaded from Bioconductor http://www.bioconductor.org.
Graphic presentations of pathways are searchable at url http://www.genome.ad.jp/kegg/pathway.html by using pathway identifiers as keys.
Mappings were based on data provided by: KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15
AnnotationDb-class for use of
the select() interface.
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.
## Bimap interface:
x <- org.Hs.egPATH
# Get the entrez gene identifiers that are mapped to a KEGG pathway ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
# Get the PATH for the first five genes
xx[1:5]
# Get the first one
xx[[1]]
}
# For the reverse map:
# Convert the object to a list
xx <- as.list(org.Hs.egPATH2EG)
# Remove pathway identifiers that do not map to any entrez gene id
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
# The entrez gene identifiers for the first two elements of XX
xx[1:2]
# Get the first one
xx[[1]]
}