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.
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.
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).
Value
A list with the following elements:
callsThe list of CNV calls, including Bayes factor in favour
of the call, expected and observed number of reads and position of the
CNV call.
Details
This function fits a hidden Markov model to the read depth data with
three hidden states (normal, deletion, duplication).