hu6800CHRLOC {hu6800}R Documentation

Mappings between probe identifiers and the chromosomal locations of the genes represented by the probe identifiers

Description

hu6800CHRLOC maps probe ids to the starting positions of the genes represented by the probe ids on chromosomes. The position of a gene is measured as the number of base pairs.

Details

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). NAs are assigned to probe ids whose chromosomal locations are not known.

Since a given gene may have more than one chromosomal locations, each probe id is mapped to a named vector of length 1 or greater. The names of each vector give the chromosome number where the genes reside. When a gene can be mapped to a given chromosome but the exact location of the gene can not be determined with confidence, "random" is appended to the end of the name for a chromosomal location value.

Mappings were based on data provided by:

Golden Path:http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/. Built: hg17

Package built Thu Sep 16 11:33:39 2004

Examples

    # Covert to a list
    xx <- as.list(hu6800CHRLOC)
    # Remove probe ids that do not map to any CHRLOC
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # Gets the location for the first five probes
        xx[1:5]
        # Gets the first one
        xx[[1]]
    }

[Package hu6800 version 1.6.5 Index]