# Calls Copy Number Variants from Targeted Sequence Data

## Documentation for package ‘ExomeDepth’ version 1.1.15

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

AnnotateExtra | AnnotateExtra
AnnotateExtra-method | AnnotateExtra
CallCNVs | CallCNVs
CallCNVs-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.
C_hmm | C_hmm
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.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-method | ExomeDepth initialization tool
plot-method | Plotting function for ExomeDepth objects
plot-methods | Plotting function for ExomeDepth objects
plot.ExomeDepth | 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 | TestCNV
TestCNV-method | TestCNV
viterbi.hmm | Computes the Viterbi path for a hidden markov model