calculate.CN {ioncopy}

Calculation of copy numbers

Description

Starting from a matrix of coverages, the corresponding matrix of copy numbers is calculated. The caluculation includes a sample normalization step and a amplicon normalization step.

Usage

calculate.CN(coverage, scale.amplicon=NULL)

Arguments

coverage

A numeric matrix containing the coverages of each amplicon (rows) in each sample (columns).

scale.amplicon

Method for amplicon normalization. If NULL the scaling factors are estimated from coverage.

Value

Matrix of copy numbers with the amplicon scaling factors ("scale.amplicon") as attribute.

Examples

## Not run: 
data(coverage)
CN <- calculate.CN(coverage)

## End(Not run)