GOLL2GO {GO}R Documentation

Aannotation of LocusLink identifiers to the GO identifiers corresponding to the genes represented by the LocusLink identifiers

Description

This is an R environment (hash table) mapping LocusLink ids to GO ids corresponding the genes represented by the LocusLink identifiers

Details

LocusLink ids are keys and the corresponding GO ids are values. Values are named vectors of length 1 or greater depending on whether a given LocusLink id can be mapped to only one or more GO ids. Names for values are the evidence codes for the GO ids (if evidence code was provided by source data). 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

NA is assigned to LocusLink id that can not be mapped to any GO id at this time.

Mappings were based on data provided by:

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

http://www.ncbi.nlm.nih.gov/LocusLink

Examples

        require("GO") || stop("GO unavailable")
        # Convert the environment object to a list
        xx <- as.list(GOLL2GO)
        # Remove LocusLink ids that are not mapped to any GO id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
                # Get the GO ids for the first two elents of xx
                goids  <- xx[1:2]
                # Get the evidence code goids
                evds <- sapply(goids, names)
        }

[Package GO version 1.5.1 Index]