annaffyGO {annaffy}R Documentation

Subset of annotation data file for GO in the hgu95av2 package

Description

This is an R environment (hash table lilke) object containing key and value pairs for the mappings between probe identifiers (key) and Gene Ontology information collected from Gene Ontology consortium. Keys can be accessed using ls(name of the environment) and values using get(key, name of the environment) or multiget(keys, name of the environment). Each probe id is mapped to a list of one (mapped to none or one GO id) or more (mapped to more than one GO ids) elements. When a probe id is mapped to at lest one GO id, each element of the list contains a sub list of three elements named "GOID", "Ontology", and "Evidence". Values for element "GOID" gives the Gene Ontology identifiers the key probe ids corresponding to. Values for element "Ontology" can be an abbreviation of MF (mocular function), BP (biological process), or CC (cellular component) for the GO category the GO id belongs to. Values for element "Evidence" contains an evidence code indicating what kind of evidence is found to support the association of the GO id to the key probe id. 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

Mappings between probe ids and GO ids were obtained through their mappings to LocusLink ids. NA is assigned to probe identifiers that can not be mapped to any Gene Ontology id at this time. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO.

Details

Mappings were based on data provided by LocusLink

Source data built: LocusLink built: January 13, 2004.ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Package built: Wed Jan 14 22:11:05 2004 Contains 250 randomly selected probes

References

ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz

Examples

        require("annotate") || stop("annotate unavailable")
        xx <- ls(env = annaffyGO)
        if(length(xx) > 0){
                # Using get for value of the first key
                get(xx[1], annaffyGO )
                #Using multiget for a few keys
                if(length(xx) >= 3){
                        multiget(xx[1:3], annaffyGO )
                        #Using lookUp of annotate(> 1.3.4)
                        lookUp(xx[1:3],"annaffy","GO")
                }
                # Get GO ids. annotate >= 1.3.7
                goids <- lookUp(ls(annaffyGO)[1], "annaffy", "GO")
                if(!is.na(goids)){
                    # GO id of the first element
                    goids[[1]]$GOID
                    # Ontology category of the first element
                    goids[[1]]$Ontology
                    # Evidence code
                    goids[[1]]$Evidence
                }
        }

[Package annaffy version 1.0.7 Index]