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)

[Package acnr version 1.0.0 Index]