| hgu95av2PATH {hgu95av2.db} | R Documentation |
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms.
hgu95av2PATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved
hgu95av2PATH2PROBE is an R object that provides mappings between KEGG identifiers and manufacturer identifiers.
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 <- hgu95av2PATH
# Get the probe identifiers that are mapped to a KEGG pathway ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the PATH for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
# Now convert the hgu95av2PATH2PROBE object to a list
xx <- as.list(hgu95av2PATH2PROBE)
if(length(xx) > 0){
# Get the probe identifiers for the first two pathway identifiers
xx[1:2]
# Get the first one
xx[[1]]
}