hgu133aGO2ALLPROBES {hgu133a}R Documentation

Annotation of GO identifiers by all probe ids corresponding to the GO ids

Description

A GO id can be associated with a group of genes directly or indirectly through the children GO ids. hgu133aGO2ALLPROBES maps GO ids to genes (represented by probe ids) that are directly or indirectly mapped to the GOs through various approaches

Details

hgu133aGO2ALLPROBES is an environment object with key and value pairs. Keys are GO ids and values are all the probe ids that are mapped to the GO ids directly or indirectly. 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:

LocusLink built: March 3, 2004. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga

Package built Wed Mar 3 16:27:29 2004

References

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

Examples

    # Convert to a list
    xx <- as.list(hgu133aGO2ALLPROBES)
    if(length(xx) > 0){
        # Gets the probe ids for the top 2nd and 3nd GO ids
        goids <- xx[2:3]
        # Gets all the probe ids for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }

[Package hgu133a version 1.5.1 Index]