| exomeCopy-package | Copy number variant detection from exome sequencing read depth |
| 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-class | Class "ExomeCopy" |
| 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-method | Class "ExomeCopy" |
| plot.ExomeCopy | Plot function for exomeCopy |
| plotCompiledCNV | Plot compiled CNV segments for one sequence/chromosome |
| show-method | Class "ExomeCopy" |
| subdivideGRanges | Subdivide ranges of a GRanges object into nearly equal width ranges |
| viterbiPath | Generalized negative log likelihood and Viterbi algorithms |