rat2302CHRLOC {rat2302.db} | R Documentation

## Map Manufacturer IDs to Chromosomal Location

### Description

rat2302CHRLOC is an R object that maps manufacturer 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 manufacturer identifier maps to a named vector of chromosomal locations, where the name indicates the chromosome. Due to inconsistencies that may exist at the time the object was built, these vectors may contain more than one chromosome and/or location. If the chromosomal location is unknown, the vector will contain an `NA`.

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/currentGenomes/Rattus_norvegicus ) on 2006-Jun20

### Examples

            x <- rat2302CHRLOC
            # Get the probe identifiers that are mapped to chromosome locations
            mapped_probes <- mappedkeys(x)
            # Convert to a list
            xx <- as.list(x[mapped_probes])
            if(length(xx) > 0) {
              # Get the CHRLOC for the first five probes
              xx[1:5]
              # Get the first one
              xx[[1]]
            }

[Package rat2302.db version 2.2.5 Index]