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ExomeDepth (version 1.1.10)

Calls Copy Number Variants from Targeted Sequence Data

Description

Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

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Version

Install

install.packages('ExomeDepth')

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Version

1.1.10

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

May 15th, 2016

Functions in ExomeDepth (1.1.10)

ExomeDepth-class

Class ExomeDepth

CallCNVs

Call CNV data from an ExomeDepth object.

AnnotateExtra

Add annotations to a ExomeDepth object

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

count.everted.reads

Count the number of everted reads for a set of BAM files.

ExomeCount

Example dataset for ExomeDepth

TestCNV

Computes the Bayes Factor in favour of a CNV defined by position and type.

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

show-methods

~~ Methods for Function show ~~

exons.hg19.X

Positions of exons on build hg19 of the human genome and on chromosome X

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

plot-methods

Plotting function for ExomeDepth objects

genes.hg19

Positions of genes on build hg19 of the human genome

qbetabinom

Quantile for betabin function

viterbi.hmm

Computes the Viterbi path for a hidden markov model

getBamCounts

Get count data for multiple exomes

select.reference.set

Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

exons.hg19

Positions of exons on build hg19 of the human genome

initialize-methods

~~ Methods for Function initialize ~~

qbetabinom.ab

Quantile function for the beta-binomial distribution

Conrad.hg19.common.CNVs

Conrad et al common CNVs

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

countBam.everted

Counts everted reads from a single BAM file