Calls Copy Number Variants from Targeted Sequence Data

---

Documentation for package ‘ExomeDepth’ version 1.1.16

• 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