⚠️There's a newer version (1.1.16) of this package.Take me there.

ExomeDepth (version 1.0.0)

Calls CNV from exome sequence data

Description

Calls copy number variants (CNVs) from targeted sequence data

Copy Link

Version

Install

install.packages('ExomeDepth')

Monthly Downloads

109

Version

1.0.0

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

February 12th, 2014

Functions in ExomeDepth (1.0.0)

ExomeCount

Example dataset for ExomeDepth

plot-methods

~~ Methods for Function plot ~~

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

TestCNV

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

CallCNVs

Call CNV data from an ExomeDepth object.

Conrad.hg19.common.CNVs

Conrad et al common CNVs

count.everted.reads

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

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

ExomeDepth-class

Class ExomeDepth

initialize-methods

~~ Methods for Function initialize ~~

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

show-methods

~~ Methods for Function show ~~

countBam.everted

Counts everted reads from a single BAM file

viterbi.hmm

Computes the Viterbi path for a hidden markov model

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

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

qbetabinom

Quantile for betabin function

AnnotateExtra

Add annotations to a ExomeDepth object

getBamCounts

Get count data for multiple exomes

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

qbetabinom.ab

Quantile function for the beta-binomial distribution

genes.hg19

Positions of genes on build hg19 of the human genome

select.reference.set

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