hgu95av2MAP {hgu95av2}R Documentation

Map between Manufacturer Identifiers and cytogenetic maps/bands

Description

hgu95av2MAP is an R environment that provides mappings between manufacturer ids and cytoband locations.

Details

Each manufacturer id is mapped to a vector of cytoband locations. The vector length may be one or longer, if there are multiple reported chromosomal locations for a given gene. An NA is reported for any manufacturer ids that cannot be mapped to a cytoband at this time.

Cytogenetic bands for most higher organisms are labeled p1, p2, p3, q1, q2, q3 (p and q are the p and q arms), etc., counting from the centromere out toward the telomeres. At higher resolutions, sub-bands can be seen within the bands. The sub-bands are also numbered from the centromere out toward the telomere. Thus, a label of 7q31.2 indicates that the band is on chromosome 7, q arm, band 3, sub-band 1, and sub-sub-band 2.

The physical location of each band on a chromosome can be obtained from another environment named "organism"CYTOLOC in a separate data package for human(humanCHRLOC), mouse(mouseCHRLOC), and rat(ratCHRLOC).

Mappings were based on data provided by:

Entrez Gene:http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Tue Oct 4 21:15:59 2005

Package built Tue Oct 4 21:31:35 2005

References

http://www.ncbi.nlm.nih.gov

Examples

    # Convert the environment to a list
    xx <- as.list(hgu95av2MAP)
    # Remove probe ids that do not map to any cytoband
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The cytobands for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    }

[Package hgu95av2 version 1.10.0 Index]