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

ExomeDepth (version 1.0.7)

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

1.0.7

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

July 20th, 2014

Functions in ExomeDepth (1.0.7)

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

count.everted.reads

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

qbetabinom.ab

Quantile function for the beta-binomial distribution

ExomeDepth-class

Class ExomeDepth

getBamCounts

Get count data for multiple exomes

show-methods

~~ Methods for Function show ~~

plot-methods

~~ Methods for Function plot ~~

exons.hg19.X

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

ExomeCount

Example dataset for ExomeDepth

TestCNV

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

CallCNVs

Call CNV data from an ExomeDepth object.

viterbi.hmm

Computes the Viterbi path for a hidden markov model

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

qbetabinom

Quantile for betabin function

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

Conrad.hg19.common.CNVs

Conrad et al common CNVs

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

initialize-methods

~~ Methods for Function initialize ~~

exons.hg19

Positions of exons on build hg19 of the human genome

countBam.everted

Counts everted reads from a single BAM file

genes.hg19

Positions of genes on build hg19 of the human genome

AnnotateExtra

Add annotations to a ExomeDepth object

select.reference.set

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

somatic.CNV.call

Call somatic variants between healthy and disease tissues.