GSE29172_H1395 {acnr}

Annotated copy-number regions from the GEO GSE29172 (and GSE26302) data sets.

Description

The GEO GSE29172 data set is a dilution series from the Affymetrix GenomeWideSNP_6 chip type. The GEO GSE26302 data set contains the experiment corresponding to the matched normal (i.e. 0% dilution).

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

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/GSE29172' directory of this package. This processing includes normalization of the raw CEL files using the CRMAv2 method implemented in the aroma.affymetrix package.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29172 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26302

References

Rasmussen, M., Sundstr\"om, M., Kultima, H. G., Botling, J., Micke, P., Birgisson, H., Glimelius, B. & Isaksson, A. (2011). Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity. Genome Biology, 12(10), R108.#'

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.

Examples

dat <- loadCnRegionData("GSE29172_H1395")
unique(dat$region)