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ExomeDepth (version 1.1.1)

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')

Monthly Downloads

109

Version

1.1.1

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

January 14th, 2015

Functions in ExomeDepth (1.1.1)

initialize-methods

~~ Methods for Function initialize ~~

AnnotateExtra

Add annotations to a ExomeDepth object

Conrad.hg19.common.CNVs

Conrad et al common CNVs

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

CallCNVs

Call CNV data from an ExomeDepth object.

count.everted.reads

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

show-methods

~~ Methods for Function show ~~

select.reference.set

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

qbetabinom

Quantile for betabin function

exons.hg19.X

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

viterbi.hmm

Computes the Viterbi path for a hidden markov model

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

countBam.everted

Counts everted reads from a single BAM file

exons.hg19

Positions of exons on build hg19 of the human genome

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

qbetabinom.ab

Quantile function for the beta-binomial distribution

ExomeDepth-class

Class ExomeDepth

genes.hg19

Positions of genes on build hg19 of the human genome

getBamCounts

Get count data for multiple exomes

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

ExomeCount

Example dataset for ExomeDepth

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

plot-methods

Plotting function for ExomeDepth objects

TestCNV

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