acnr (version 1.0.0)

loadCnRegionData: loadCnRegionData

Description

Load real, annotated copy number data

Usage

loadCnRegionData(dataSet, tumorFraction = 1)

Arguments

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.

Value

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).

Details

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

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)