| cytoband-data {RCytoGPS} | R Documentation |
Example Cytoband Data
Description
This data set contains the genomic locations of cytobands along with loss-gain-fusion percentages for three group of samples.
Usage
data(cytoData)
Format
A data matrix (cytobandLocations) containing 868 rows and
14 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 first five columns are the
same as in the cytobandLocations data set. The remaining
nine columns form three sets of three, recording the percentage of Loss,
Gain, and Fusion events in three sets of samples, labeled "A", "B",
and "C".
Author(s)
Kevin R. Coombes krc@silicovore.com, Dwayne G. Tally dtally110@hotmail.com
Source
The cytoband locations were downloaded from the UCSC Genome Browser and synchronized with the list of cytobands in ISCN 2016. The percentages were computed using tools in this package from subsets of the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer.
References
J. McGowan-Jordan, A. Simons, M. Schmid (editors). ISCN 2016: An International System for Human Cytogenomic Nomenclature. Karger Publishing, Basel, 2016.
Mitelman, F., B. Johansson, and F. Mertens, Catalog of chromosome aberrations in cancer. Vol. 1. 1991: Wiley-Liss New York.