calculateCopyNumber {oligoClasses}R Documentation

Calculates copy number as the average of SNP-level summaries from the A and B alleles

Description

Calculates copy number as the average of SNP-level summaries from the A and B alleles from an object of class SnpCallSetPlus

Usage

calculateCopyNumber(object, ...)

Arguments

object an instance of SnpCallSetPlus
... Not implemented

Details

The average A (and B) allele intensities for each SNP is centered by the median intensity across samples (should have a reasonable (e.g., > 10) samples). Addtionally, we assume that the median intensity across all samples for autosomes should be the same for homozygous genotypes and heterozygous geneotypes. The resulting intensities are then recentered at 2 copies (for autosomes), 1 for the male X chromosome, 2 for the female X, etc. We assume that for a given SNP, the median copy number is normal. If this is not likely to be the case, alternative approaches should be explored.

Value

A matrix of copy number intensities.

Author(s)

R. Scharpf

See Also

SnpCallSetPlus-class


[Package oligoClasses version 1.4.0 Index]