Normalize allele-specific copy numbers (total,fracB)

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Description

Normalize allele-specific copy numbers (total,fracB), where total is the total (non-polymorphic) signal and fracB is the allele B fraction. It is only loci with a non-missing (NA) fracB value that are considered to be SNPs and normalized by CalMaTe. The other loci are left untouched.

Usage

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## S3 method for class 'matrix'
snpsNByTotalAndFracB(data, references=NULL, ..., verbose=FALSE)

Arguments

data

An Jx2xI numeric array, where J is the number of loci, 2 is total and fracB, and I is the number of samples.

references

A logical or numeric vector specifying which samples should be used as the reference set. By default, all samples are considered.

...

Additional arguments passed to fitSNPsN.

verbose

See Verbose.

Value

Returns an Jx2xI numeric array.