zebrafishACCNUM {zebrafish}R Documentation

Mappings between probe identifiers and manufacturer or user provided identifiers

Description

zebrafishACCNUM contains mappings between probe ids to identifiers provided by a manufacturer or user at the time when zebrafish was built. The manufacture or user provided ids were used to link probe ids to annotation data available from various public data sources to obtain the other annotations contained in zebrafish.

Details

In order to build an annotate data package, a data file with a column for probe ids and another for the matching manufacturer/user provided ids is required. This data file is used as the base for mapping probe ids to LocusLink identifiers (unique ids used by NCBI http://www.ncbi.nlm.nih.gov/LocusLink/ to represent genetic loci and link to curated sequence and descriptive information) through the manufacturer/user provided ids. The mapped LocusLink ids then serve as the point of linkage to other annotation data provided by various public data sources.

zebrafishACCNUM contains the mappings of the base file and the derived mappings between probe ids to other annotation data are contained by other annotation data files in zebrafish.

Valid manufacturer/user provided ids currently include GenBank accession numbers (identifiers obtained after submitting a sequence to GenBank, EMBL or DDBJ), UniGene ids (identifiers used by NCBI to represent clusters of sequences of a unique gene), RefSeq ids (identifiers for non-redundant sequences curated by NCBI), or IMAGE clone ids (identifies given to clones from shared arrayed cDNA libraries by The Integrated Molecular Analysis of Gene Expression (IMAGE) Consortium).

For all the Affymetrix chips, the manufacturer/user provided ids are GenBank accession numbers.

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

Examples

        # Convert to a list
        xx <- as.list(zebrafishACCNUM)
        # Remove probe ids that do not map to any ACCNUM
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
        # Get the ACCNUM for the first five probes
        xx[1:5]
        # Get the first one
        xx[[1]]
}

[Package zebrafish version 1.6.5 Index]