GSE11976_CRL2324: Annotated copy-number regions from the GEO GSE11976 data set.
In mpierrejean/acnr: Annotated Copy-Number Regions

Description Format Details Examples

The GEO GSE11976 data set is a dilution series from the Illumina HumanCNV370v1 chip type (Staaf et al, 2008).

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.

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.