getMinorMajorCopyNumbers {acnr}

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

region

A character value, the annotation label for a copy number region. Should be encoded as "(C1,C2)", where

C1

denotes the minor copy number, that is, the smallest of the two parent-specific copy numbers

C2

denotes the minor copy number, that is, the smallest of the two parent-specific copy numbers

Value

A matrix with length(region) rows and two columns: C1 and C2, 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) Statistical analysis 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)