AnnotateExtra           Add annotations to a ExomeDepth object
AnnotateExtra-methods   Additional annotations for ExomeDepth objects
CallCNVs                Call CNV data from an ExomeDepth object.
Conrad.hg19.common.CNVs
                        Conrad et al common CNVs
ExomeCount              Example dataset for ExomeDepth
ExomeDepth-class        Class 'ExomeDepth'
ExomeDepth-package      Read depth based CNV calls for exome DNA
                        sequence data
TestCNV                 Computes the Bayes Factor in favour of a CNV
                        defined by position and type.
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
initialize-methods      ~~ Methods for Function 'initialize' ~~
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.
show-methods            ~~ Methods for Function 'show' ~~
somatic.CNV.call        Call somatic variants between healthy and
                        disease tissues.
viterbi.hmm             Computes the Viterbi path for a hidden markov
                        model
