ath1121501PATH {ath1121501} | R Documentation |
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. ath1121501PATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved
Each KEGG pathway has a name and id. Pathway name for a given pathway id 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 ids as keys.
Mappings were based on data provided by:
Tair: ftp://ftp.arabidopsis.org/home/tair/Pathways/aracyc_dump_20060214 Built: N/A
Tair: ftp://ftp.arabidopsis.org/home/tair/Genes/gene_aliases.20051208 Tair: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes Tair: ftp://ftp.arabidopsis.org/home/tair/Ontologies/Plant_Ontology/stru-060309.txt Built: N/A
Package built Tue Jun 13 12:55:18 2006
# Convert the environment to a list xx <- as.list(ath1121501PATH) # Remove probe ids that do not map to any pathway id xx <- xx[!is.na(xx)] if(length(xx) > 0){ # The pathway ids for the first two elements of XX xx[1:2] # Get the first one xx[[1]] }