GSE11976_CRL2324 {acnr}

R Documentation

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).

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.

Examples

dat <- loadCnRegionData("GSE11976_CRL2324")
unique(dat$region)

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