AnnotateExtra,ExomeDepth-method
                        AnnotateExtra
C_hmm                   C_hmm
CallCNVs,ExomeDepth-method
                        CallCNVs
Conrad.hg19.common.CNVs
                        Conrad et al common CNVs
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.
ExomeCount              Example dataset for ExomeDepth
ExomeDepth-class        Class 'ExomeDepth'
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_loglike_matrix      get_loglike_matrix
get.power.betabinom     Estimate the power to compare two beta-binomial
                        distributions.
getBamCounts            Get count data for multiple exomes
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
TestCNV,ExomeDepth-method
                        TestCNV
viterbi.hmm             Computes the Viterbi path for a hidden markov
                        model
