ratCHRLOC1END {ratCHRLOC}R Documentation

An annotation data file for transciption ending location of genes on chromosome 1

Description

ratCHRLOC1END mapps LocusLink ids to the transciption ending location of genes on chromosome number 1 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 ending location for genes. The ending 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 largest end 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(ratCHRLOC1END)
        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]