agPATH2PROBE {ag} | R Documentation

## Map between Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway identifiers and Manufacturer Identifiers

### Description

agPATH2PROBE is an R environment that provides mappings between KEGG identifiers and manufacturer identifiers.

### Details

Each KEGG identifier is mapped to a named vector of manufacturer identifiers. The name represents the KEGG identifier and the vector contains all manufacturer identifiers that are found in that particular pathway. An `NA` is reported for any KEGG identifier that cannot be mapped to any manufacturer identifiers.

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 http://www.genome.ad.jp/kegg/pathway.html using pathway identifiers as keys.

Mappings were based on data provided by:

Tair: ftp://ftp.arabidopsis.org/home/tair//ath/ath_gene_map.tab Built: N/A

Tair: ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt Tair: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes Tair: ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.08012006.txt Built: N/A

Package built Wed Sep 6 11:22:37 2006

### References

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

### Examples

        # Convert the environment to a list
        xx <- as.list(agPATH2PROBE)
        # Remove pathway identifiers that do not map to any probe id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
            # The probe identifiers for the first two elements of XX
            xx[1:2]
            # Get the first one
            xx[[1]]
        }

[Package ag version 1.14.0 Index]