loadCnRegionData: loadCnRegionData
In acnr: Annotated Copy-Number Regions

Description Usage Arguments Details Value Author(s) Examples

Load real, annotated copy number data

1	loadCnRegionData(dataSet, tumorFraction = 1)

`dataSet`	name of one of the data sets of the package, see `listDataSets`
`tumorFraction`	proportion of tumor cells in the "tumor" sample (a.k.a. tumor cellularity). See `listTumorFractions`.

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

* a dilution series from the Affymetrix GenomeWideSNP_6 chip type (Rasmussen et al, 2011), see GSE29172_H1395 * a dilution series from the Illumina HumanCNV370v1 chip type (Staaf et al, 2008), see GSE11976_CRL2324 * a tumor/normal pair from the Affymetrix GenomeWideSNP_6 chip type (Chiang et al, 2008), see GSE13372_HCC1143

a data.frame containing copy number data for different types of copy number 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)", 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

muN

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

Morgane Pierre-Jean and Pierre Neuvial

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)