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