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 |