GOALLENTREZID {GO} | R Documentation |
This is an R environment (hash table) mapping GO identifiers to all the Entrez Gene identifiers corresponding to the GO identifiers and its direct or indirect offspring. The direct or indirect offspring of a given GO identifier are the nodes that are directly linked to the node for the GO identifier or indirectly linked to the GO identifier through nodes that are linked to the GO identifier based on the directed acyclic graph defined by Gene Ontology Consortium
GO identifiers are Keys and the corresponding Entrez Gene identifiers are Values. Values are named vectors of length 1 or greater depending on whether a given GO identifier can be mapped to one or more Entrez Gene identifiers. Names for values are the evidence codes for the GO identifier (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 identifiers that can not be mapped to any Entrez Gene identifier at this time.
Mappings were based on data provided by:
Gene Ontology:ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest. Built: Build Information not available
Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA. Built: Source data downloaded from Entrez Gene on Mon Apr 7 09:09:28 2008
Package built: Mon Apr 7 09:09:39 2008
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(GOALLENTREZID) # Remove GO identifiers that are not mapped to any Entrez Gene identifier xx <- xx[!is.na(xx)] if(length(xx) > 0){ # Get the Entrez Gene identifiers for the first two elents of xx llids <- xx[1:2] # Get the evidence code llids evds <- sapply(llids, names) }