zebrafishLOCUSID {zebrafish}R Documentation

Mappings between probe identifiers and LocusLink identifiers

Description

LocusLink identifiers are unique ids used by NCBI http://www.ncbi.nlm.nih.gov/LocusLink/ to represent genetic loci and link to curated sequence and descriptive information. zebrafishLOCUSID maps probe identifiers to LocusLink identifiers for genes represented by the probe identifiers.

Details

Mappings of probe ids to LocusLink ids are achieved through the linkage between probe ids to manufacturer/user provided ids contained in zebrafishACCNUM. LocusLink ids are first mapped to manufacturer/user provided ids using file(s) provided by Locuslink and in some cases UniGene and other available sources and then linked to probe ids based on the mappings between probe ids and manufacturer/user provided ids.

When a given probe id was mapped to different LocusLink ids by different sources, the one agreed by most sources was selected. When no agreement was achieved among sources, the one of the smallest numeric value was selected.

Mappings were based on data provided by:

LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: September 16, 2004

Package built: Fri Sep 17 09:37:03 2004

References

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

Examples

    # Convert the environment to a list
    xx <- as.list(zebrafishLOCUSID)
    # Remove probe ids that do not map to any LOCUSID
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The LOCUSIDs for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    }

[Package zebrafish version 1.6.5 Index]