YEASTPATH2PROBE {YEAST} | R Documentation |
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. Each pathway has a name, pathway id, and graphical presentation of the pathway. YEASTPATH2PROBE maps KEGG pathway ids to probe identifiers representing genes whose products participate in the interactions of the pathway
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} using pathway ids as keys.
Mappings were based on data provided by:
KEGG:ftp://ftp.genome.ad.jp/pub/kegg/pathways. Built: Yeast Genome data are built at various time intervals. Sources used were downloaded Fri Jan 7 14:56:44 2005
Yeast Genome:http://www.yeastgenome.org/DownloadContents.shtml. Built: Yeast Genome data are built at various time intervals. Sources used were downloaded Fri Jan 7 14:56:40 2005
Package built Fri Jan 7 16:12:38 2005
# Convert the environment to a list xx <- as.list(YEASTPATH2PROBE) # Remove pathway ids that do not map to any probe id xx <- xx[!is.na(xx)] if(length(xx) > 0){ # The probe ids for the first two elements of XX xx[1:2] # Get the first one xx[[1]] }