ratCHRLOC12START {ratCHRLOC}R Documentation

An annotation data file for transciption starting locations of genes on chromosome 12

Description

ratCHRLOC12START maps LocusLink ids to the transciption starting locations of genes on chromosome number 12 corresponding to the LocusLink ids

Details

This is an environment object containing key and value pairs. Keys are LocusLink ids and values are the transciption starting location for genes. The starting positions for genes on both the sense and antisense strand are number of base pairs measured from the p (5' end of the sense strand) to q (3' end of the sense strand) arms. Values for the antisense strand have a leading "-" sign (e. g. -1234567).

Values for keys are named vectors of length 1 derived from the smallest starting value found for the LocusLink id. Names of chromosome location values can be "Confident" when the gene can be confidently placed on a chromosome and "Unconfident" otherwise (denoted by "_random" in UCSC data).

Mappings were derived from the following public data sources:

Golden Path:http://gopher5/compbio/annotationSourceData/hgdownload.cse.ucsc.edu/goldenPath/currentGenomes//Rattus_norvegicus/database/. Built: No build info available.

Package built: Sat Mar 25 23:23:04 2006

References

http://www.genome.ucsc.edu/goldenPath/hg16/database/

Examples

        require("annotate") || stop("annotate unavailable")
        xx <- as.list(ratCHRLOC12START)
        if(length(xx) > 0){
                # Get the value of the first key
                xx[1]
                # Get the values for a few keys
                if(length(xx) >= 3){
                    xx[1:3]
                }
        }

[Package ratCHRLOC version 1.12.0 Index]