ExomeCopy-class         Class "ExomeCopy"
compileCopyCountSegments
                        Compile segments across samples
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-package       Copy number variant detection from exome
                        sequencing read depth
exomecounts             Sample counts from 16 exome sequencing samples
                        from 1000 Genomes Project
generateBackground      Generate median background read depth
getGCcontent            Get the GC content of target ranges from a
                        reference FASTA file
negLogLike              Generalized negative log likelihood and Viterbi
                        algorithms
plot.ExomeCopy          Plot function for exomeCopy
plotCompiledCNV         Plot compiled CNV segments for one
                        sequence/chromosome
subdivideGRanges        Subdivide ranges of a GRanges object into
                        nearly equal width ranges
