hgu133aGO2PROBE {hgu133a} | R Documentation |
A GO id can be associated with a group of genes directly. hgu133aGO2PROBE maps each GO id to the genes represented by probe ids that are directly associated with the GO id.
hgu133aGO2PROBE is an environment object with key and value pairs. Keys are GO ids and values are the probe ids that are directly or associated with the GO ids. Values are vectors of length 1 or greater depending on whether a given GO id can be mapped to only one or more probe ids. Names for values are the evidence codes for the GO ids indicating what kind of evidence is found to support the association. The evidence codes 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
GO ids can not be mapped to any probe identifier are assigned a value of NA. A GO id may be mapped to the same probe id more than once but the evidence code can be different. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO.
Mappings were based on data provided by:
LocusLink LocusLink built: March 3, 2004. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga.
Package built Wed Mar 3 16:27:29 2004
ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz
# Convert to a list xx <- as.list(hgu133aGO2PROBE) if(length(xx) > 0){ # Gets the probe ids for the top 2nd and 3nd GO ids goids <- xx[2:3] # Gets the probe ids for the first element of goids goids[[1]] # Evidence code for the mappings names(goids[[1]]) }