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Annotated Copy-Number Regions

Description

This data package contains SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.

Details

Author(s)

Morgane Pierre-Jean and Pierre Neuvial

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 thediluted tumor sample (after TumorBoost)

genotype

germlinegenotypes

region

a character value, annotation label for the region. Should beencoded as"(C1,C2)", whereC1 denotes the minor copy numberandC2 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 withLOH

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)

Annotated copy-number regions from the GEO GSE13372 data set.

Description

The GEO GSE13372 data set is from the Affymetrix GenomeWideSNP_6 chip type. We have extracted one tumor/normal pair corresponding to the breast cancer cell line HCC1143. For consistency with the other data sets in the package the tumor and normal samples are labeled according to their tumor cellularity, that is, 100

Format

A data frame with 205842 observations of 7 variables:

c

total copy number (not log-scaled)

b

allelic ratios in thediluted 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 beencoded as"(C1,C2)", whereC1 denotes the minor copy number andC2 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/GSE13372' 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=GSE13372http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13372

References

Chiang DY, Getz G, Jaffe DB, O'Kelly MJ et al. High-resolutionmapping of copy-number alterations with massively parallel sequencing. NatMethods 2009 Jan;6(1):99-103. PMID: 19043412

Bengtsson, H., Wirapati , P. & Speed, T.P. (2009). A single-arraypreprocessing 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("GSE13372_HCC1143")unique(dat$region)

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 thediluted 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 beencoded as"(C1,C2)", whereC1 denotes the minor copy number andC2 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. copynumber probes).

cellularity

A numeric value between 0 and 1, thepercentage 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 ofthis package. This processing includes normalization of the raw CEL filesusing the CRMAv2 method implemented in the aroma.affymetrix package.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29172http://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-arraypreprocessing 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 oftumor-normal genotyping microarrays. BMC bioinformatics 11 (2010), p. 245.

Examples

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

Get minor and major copy number labels from region annotation labels

Description

Get minor and major copy number labels from region annotation labels

Usage

getMinorMajorCopyNumbers(region)

Arguments

Value

Amatrix withlength(region) rows and two columns:C1 andC2, as described above.

References

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.

Neuvial, P., Bengtsson H., and Speed, T. P. (2011) Statisticalanalysis of Single Nucleotide Polymorphism microarrays in cancer studies.Chapter 11 in *Handbook of Statistical Bioinformatics*, Springer.

Examples

dat <- loadCnRegionData(dataSet="GSE29172_H1395", tumorFraction=1)regions <- unique(dat$region)getMinorMajorCopyNumbers(regions)

List available data sets

Description

List available data sets

Usage

listDataSets()

Value

name of one of the data sets of the package, seelistDataSets

Examples

listDataSets()

List of available tumor fractions for a data set

Description

List of available tumor fractions for a data set

Usage

listTumorFractions(dataSet)

Arguments

Value

A numeric vector, the available tumor fractions for a data set

Examples

dataSets <- listDataSets()fracs <- listTumorFractions(dataSets[1])

loadCnRegionData

Description

Load real, annotated copy number data

Usage

loadCnRegionData(dataSet, tumorFraction = 1)

Arguments

Details

This function is a wrapper to load real genotyping array data taken from

* a dilution series from the Affymetrix GenomeWideSNP_6 chip type (Rasmussenet al, 2011), seeGSE29172_H1395 * a dilution series from theIllumina HumanCNV370v1 chip type (Staaf et al, 2008), seeGSE11976_CRL2324 * a tumor/normal pair from the AffymetrixGenomeWideSNP_6 chip type (Chiang et al, 2008), seeGSE13372_HCC1143

Value

a data.frame containing copy number data for different types of copynumber regions. Columns:

c

Total copy number

b

Allele B fraction (a.k.a. BAF)

region

a character value,annotation label for the region. Should be encoded as"(C1,C2)",whereC1 denotes the minor copy number andC2 denotes themajor 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

muN

the (germline)genotype of SNPs. By definition, rows with missing genotypes areinterpreted as non-polymorphic loci (a.k.a. copy number probes).

Author(s)

Morgane Pierre-Jean and Pierre Neuvial

Examples

affyDat <- loadCnRegionData(dataSet="GSE29172_H1395", tumorFraction=1)str(affyDat)illuDat <- loadCnRegionData(dataSet="GSE11976_CRL2324", tumorFraction=.79)str(illuDat)affyDat2 <- loadCnRegionData(dataSet="GSE13372_HCC1143", tumorFraction=1)str(affyDat2)