loadCnRegionData: loadCnRegionData
In acnr: Annotated Copy-Number Regions

Description Usage Arguments Details Value Author(s) References Examples

Load real, annotated copy number data

1	loadCnRegionData(dataSet = c("GSE29172", "GSE11976"), tumorFraction = 1)

`dataSet`	microarray dataSet from which the data was generated.
`tumorFraction`	proportion of tumor cells in the "tumor" sample. Should be in .3, .5, .7, 1 if `dataSet=="GSE29172"`, and in .14,.34,.50,.79,1 when `dataSet=="GSE11976"`.

This function is a wrapper to load real genotyping array data taken from dilution series from the Affymetrix GenomeWideSNP_6 chip type (Rasmussen et al, 2011) or from the Illumina HumanCNV370v1 chip type (Staaf et al, 2008)

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. Preferably 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

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.

GEO data set: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976

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.

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

affyDat <- loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
str(affyDat)

illuDat <- loadCnRegionData(dataSet="GSE11976", tumorFraction=.79)
str(illuDat)