Detection of CNV in exome/targeted sequencing data

Documentation for package ‘exomeCopy’ version 1.0.3

exomeCopy-package	Detection of CNV in exome/targeted sequencing data
copyCountSegments	Segments of identical copy count from exomeCopy
countBamInGRanges	Count reads from BAM file in genomic ranges
exomeCopy	Fit the exomeCopy or exomeCopyVar model to the observed counts.
ExomeCopy-class	Class "ExomeCopy"
exomecounts	Sample counts from 16 exome sequencing samples from 1000 Genomes Project
negLogLike	Generalized negative log likelihood and Viterbi algorithms
plot-method	Class "ExomeCopy"
plot.ExomeCopy	Plot function for exomeCopy
show-method	Class "ExomeCopy"
subdivideGRanges	Subdivide ranges of a GRanges object into nearly equal width ranges
viterbiPath	Generalized negative log likelihood and Viterbi algorithms