SHDZMAP {SHDZ.db} | R Documentation

## Map between Manufacturer Identifiers and cytogenetic maps/bands

### Description

SHDZMAP is an R object that provides mappings between manufacturer identifiers and cytoband locations.

### Details

Each manufacturer identifier 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 identifiers 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 object 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 ( ftp://ftp.ncbi.nlm.nih.gov/gene/DATA ) on 2008-Sep2

### References

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

### Examples

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

[Package SHDZ.db version 2.2.5 Index]