GSE13372_HCC1143: Annotated copy-number regions from the GEO GSE13372 data set.
Description
The GEO GSE13372 data set is from the Affymetrix GenomeWideSNP_6 chip type.
We have extracted one tumor/normal pair corresponding to the breast cancer
cell line HCC1143. For consistency with the other data sets in the package
the tumor and normal samples are labeled according to their tumor
cellularity, that is, 100
Arguments
Format
A data frame with 205842 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/GSE13372' directory of
this package. This processing includes normalization of the raw CEL files
using the CRMAv2 method implemented in the aroma.affymetrix package.
References
Chiang DY, Getz G, Jaffe DB, O'Kelly MJ et al. High-resolution
mapping of copy-number alterations with massively parallel sequencing. Nat
Methods 2009 Jan;6(1):99-103. PMID: 19043412 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.