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
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).