Mappings between probe identifiers and KEGG pathway identifiers

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms.

SomaScanPATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved.

SomaScanPATH2PROBE is an R object that provides mappings between KEGG identifiers and SeqIds.

Details

Each KEGG pathway has a name and identifier. The pathway name for a given pathway identifier can be obtained using the KEGG data package that can downloaded from Bioconductor (http://www.bioconductor.org).

Graphic presentations of pathways are searchable at 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

Value

A Bimap object of the ProbeAnnDbBimap class.

References

http://www.genome.ad.jp/kegg/

See also

AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
x <- SomaScanPATH
# 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][1:300])
if(length(xx) > 0) {
    # Get the PATH for the first five probes
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#>  [1] "04010" "04012" "04062" "04270" "04370" "04510" "04540" "04650"
#>  [9] "04660" "04662" "04664" "04666" "04720" "04722" "04730" "04810"
#> [17] "04910" "04912" "04914" "04916" "05160" "05200" "05210" "05211"
#> [25] "05212" "05213" "05214" "05215" "05218" "05219" "05220" "05221"
#> [33] "05223"

x <- SomaScanPATH
mapped_probes <- mappedkeys(x)
# Now convert the SomaScanPATH2PROBE object to a list
xx <- as.list(x[mapped_probes][1:300])
if(length(xx) > 0){
    # Get the probe identifiers for the first two pathway identifiers
    xx[1:2]
    # Get the first value
    xx[[1]]
} 
#>  [1] "04010" "04012" "04062" "04270" "04370" "04510" "04540" "04650"
#>  [9] "04660" "04662" "04664" "04666" "04720" "04722" "04730" "04810"
#> [17] "04910" "04912" "04914" "04916" "05160" "05200" "05210" "05211"
#> [25] "05212" "05213" "05214" "05215" "05218" "05219" "05220" "05221"
#> [33] "05223"