Entrez Gene IDs to Chromosomal Location

Description

org.Rn.egCHRLOC is an R object that maps entrez gene identifiers to the starting position of the gene. The position of a gene is measured as the number of base pairs.

The CHRLOCEND mapping is the same as the CHRLOC mapping except that it specifies the ending base of a gene instead of the start.

Details

Each entrez gene identifier maps to a named vector of chromosomal locations, where the name indicates the chromosome.

Chromosomal locations on both the sense and antisense strands are measured as the number of base pairs from the p (5' end of the sense strand) to q (3' end of the sense strand) arms. Chromosomal locations on the antisense strand have a leading "-" sign (e. g. -1234567).

Since some genes have multiple start sites, this field can map to multiple locations.

Mappings were based on data provided by: UCSC Genome Bioinformatics (Rattus norvegicus) ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5 With a date stamp from the source of: 2012-Jun11

Examples

        x <- org.Rn.egCHRLOC
        # Get the entrez gene identifiers that are mapped to chromosome locations
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
          # Get the CHRLOC for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }