AnnotateExtra,ExomeDepth-method
                        AnnotateExtra
C_hmm                   C_hmm
CallCNVs,ExomeDepth-method
                        CallCNVs
Conrad.hg19.common.CNVs
                        Conrad et al common CNVs
ExomeCount              Example dataset for ExomeDepth
ExomeDepth-class        Class 'ExomeDepth'
TestCNV,ExomeDepth-method
                        TestCNV
count.everted.reads     Count the number of everted reads for a set of
                        BAM files.
countBam.everted        Counts everted reads from a single BAM file
countBamInGRanges.exomeDepth
                        Compute read count data from BAM files.
exons.hg19              Positions of exons on build hg19 of the human
                        genome
exons.hg19.X            Positions of exons on build hg19 of the human
                        genome and on chromosome X
genes.hg19              Positions of genes on build hg19 of the human
                        genome
get.power.betabinom     Estimate the power to compare two beta-binomial
                        distributions.
getBamCounts            Get count data for multiple exomes
get_loglike_matrix      get_loglike_matrix
initialize,ExomeDepth-method
                        ExomeDepth initialization tool
plot-methods            Plotting function for ExomeDepth objects
qbetabinom              Quantile for betabin function
qbetabinom.ab           Quantile function for the beta-binomial
                        distribution
select.reference.set    Combine multiple samples to optimize the
                        reference set in order to maximise the power to
                        detect CNV.
somatic.CNV.call        somatic.CNV.call
viterbi.hmm             Computes the Viterbi path for a hidden markov
                        model
