GSE29172_H1395: Annotated copy-number regions from the GEO GSE29172 (and GSE26302) data sets.
Description
The GEO GSE29172 data set is a dilution series from the Affymetrix
GenomeWideSNP_6 chip type. The GEO GSE26302 data set contains the experiment
corresponding to the matched normal (i.e. 0% dilution).
Arguments
Format
A data frame with 770668 observations of 7 variables:
c
total copy number (not log-scaled)
b
allelic ratios in the
diluted tumor sample (after TumorBoost)
genotype
germline
genotypes
bT
allelic ratios in the diluted tumor sample (before
TumorBoost)
bN
allelic ratios in the matched normal sample
region
a character value, annotation label for the region. Should be
encoded as "(C1,C2)", where C1 denotes the minor copy number
and C2 denotes the major copy number. For example,
(1,1)
Normal
(0,1)
Hemizygous deletion
(0,0)
Homozygous deletion
(1,2)
Single copy gain
(0,2)
Copy-neutral LOH
(2,2)
Balanced two-copy gain
(1,3)
Unbalanced two-copy gain
(0,3)
Single-copy gain with
LOH
genotype
the (germline) genotype of SNPs. By definition, rows
with missing genotypes are interpreted as non-polymorphic loci (a.k.a. copy
number probes).
cellularity
A numeric value between 0 and 1, the
percentage of tumor cells in the sample.
Details
These data have been processed from the files available from GEO using
scripts that are included in the 'inst/preprocessing/GSE29172' directory of
this package. This processing includes normalization of the raw CEL files
using the CRMAv2 method implemented in the aroma.affymetrix package.
References
Rasmussen, M., Sundstr\"om, M., Kultima, H. G., Botling, J.,
Micke, P., Birgisson, H., Glimelius, B. & Isaksson, A. (2011).
Allele-specific copy number analysis of tumor samples with aneuploidy and
tumor heterogeneity. Genome Biology, 12(10), R108.#' Bengtsson, H., Wirapati , P. & Speed, T.P. (2009). A single-array
preprocessing method for estimating full-resolution raw copy numbers from
all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6,
Bioinformatics 25(17), pp. 2149-56. Bengtsson H., Neuvial, P. and Speed, T. P. (2010) TumorBoost:
normalization of allele-specific tumor copy numbers from a single pair of
tumor-normal genotyping microarrays. BMC bioinformatics 11 (2010), p. 245.