GSE11976_CRL2324: Annotated copy-number regions from the GEO GSE11976 data set.
Description
The GEO GSE11976 data set is a dilution series from the Illumina
HumanCNV370v1 chip type (Staaf et al, 2008).
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
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
cellularity
A numeric value between 0 and 1, the percentage of tumor cells in the sample.
@source http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976
@references Staaf, J., Lindgren, D., Vallon-Christersson, J., Isaksson, A.,
Goransson, H., Juliusson, G., ... & Ringn\'er, M. (2008).
Segmentation-based detection of allelic imbalance and
loss-of-heterozygosity in cancer cells using whole genome SNP arrays.
Genome Biol, 9(9), R136.
Details
These data have been processed from the files available at
http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/ using scripts that
are included in the 'inst/preprocessing/GSE11976' directory of this package.