ExomeDepth (version 1.0.7)

CallCNVs: Call CNV data from an ExomeDepth object.

Description

The function must be called on an ExomeDepth object. Likelihood data must have been precomputed which should have been done by default when the ExomeDepth object was created.

Usage

CallCNVs(x, chromosome, start, end, name, transition.probability =
0.0001, expected.CNV.length = 50000)

Arguments

x

An ExomeDepth object

chromosome

Chromosome information for each exon (factor).

start

Start (physical position) of each exon (numeric, must have the same length as the chromosome argument).

end

End (physical position) of each exome (numeric, must have the same length as the chromosome argument).

name

Name of each exon (character or factor).

transition.probability

Transition probability of the hidden Markov Chain from the normal copy number state to either a deletion or a duplication. The default (0.0001) expect approximately 20 CNVs genome-wide.

expected.CNV.length

The expectation for the length of a CNV. This value factors into the Viterbi algorithm that is used to compte the transition from one state to the next, which depends on the distance between exons.

Value

• The same ExomeDepth object provided as input but with the slot CNVcalls containing a data frame with the output of the calling.

Details

This function fits a hidden Markov model to the read depth data with three hidden states (normal, deletion, duplication).