01-cytoData: Cytoband Locations

In CytoGPS: Using Cytogenetics Data in R

Description

This data set contains the genomic locations of cytobands based on both the latest build of the human genome (GRch38) and the latest update to the International Standard for human Cytogenomic Nomenclature (ISCN).

Usage

data(cytobandLocations)

Format

A data matrix (cytobandLocations) containing 868 rows and 5 columns. Each row contains one of the cytobands defined in the 2016 update to ISCN nomenclature. The rownames are the standard cytoband names; for example, 1p36.33. The columns are

Chromosome

The name of the human chromosome, stored as chr#.

loc.start

The starting base position of the band.

loc.end

The ending base position of the band.

Band

The band name without the chromosome; for example, p36.33.

Stain

A factor containing the name of the Giemsa-stain color of the band in a karyotype image.

Also, a vector (idiocolors) of length eight that translates the Giemsa stain names into appropriate colors.

Source

The starting point for these data were the cytoband locations downloaded from the UCSC Genome Browser. We confirmed that the data were unchanged between human genome builds GRCh36 (hg18), GRCh37 (hg19), and GRCh38. However, the list of cytobands from UCSC was not consistent with the list of cytobands in ISCN 2016. We manually edited the source file to be compliant. It also matches the list of cytobands produced at http://cytogps.org.

References

J. McGowan-Jordan, A. Simons, M. Schmid (editors). ISCN 2016: An International System for Human Cytogenomic Nomenclature. Karger Publishing, Basel, 2016.

CytoGPS documentation built on Oct. 16, 2019, 3:01 p.m.