GOALLLOCUSID {GO} | R Documentation |
This is an R environment (hash table) mapping GO ids to all the Entrez Gene ids corresponding to the GO id and its direct or indirect offspring. The direct or indirect offspring of a given GO id are the nodes that are directly linked to the node for the GO id or indirectly linked to the GO id through nodes that are linked to the GO id based on the directed acyclic graph defined by Gene Ontology Consortium
GO ids are Keys and the corresponding Entrez Gene ids are Values. Values are named vectors of length 1 or greater depending on whether a given GO id can be mapped to one or more Entrez Gene ids. Names for values are the evidence codes for the GO id (if an evidence code was provided by source data). The evidence codes that are in use include:
IMP - inferred from mutant phenotype
IGI - inferred from genetic interaction
IPI - inferred from physical interaction
ISS - inferred from sequence similarity
IDA - inferred from direct assay
IEP - inferred from expression pattern
IEA - inferred from electronic annotation
TAS - traceable author statement
NAS - non-traceable author statement
ND - no biological data available
IC - inferred by curator
NA is assigned to GO ids that can not be mapped to any Entrez Gene id at this time.
Mappings were based on data provided by:
Gene Ontology:http://gopher5/compbio/annotationSourceData/archive.godatabase.org/latest/. Built: 15-Mar-2006
Entrez Gene:http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Fri Mar 24 17:25:12 2006
Package built: Fri Mar 24 17:25:12 2006
http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
require("GO") || stop("GO unavailable") # Convert the environment object to a list xx <- as.list(GOALLLOCUSID) # Remove GO ids that are not mapped to any Entrez Gene id xx <- xx[!is.na(xx)] if(length(xx) > 0){ # Get the Entrez Gene ids for the first two elents of xx llids <- xx[1:2] # Get the evidence code llids evds <- sapply(llids, names) }