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ExomeDepth (version 1.1.8)

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

1.1.8

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

January 5th, 2016

Functions in ExomeDepth (1.1.8)

ExomeDepth-class

Class ExomeDepth

AnnotateExtra

Add annotations to a ExomeDepth object

show-methods

~~ Methods for Function show ~~

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

countBam.everted

Counts everted reads from a single BAM file

genes.hg19

Positions of genes on build hg19 of the human genome

qbetabinom.ab

Quantile function for the beta-binomial distribution

plot-methods

Plotting function for ExomeDepth objects

select.reference.set

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

viterbi.hmm

Computes the Viterbi path for a hidden markov model

TestCNV

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

initialize-methods

~~ Methods for Function initialize ~~

qbetabinom

Quantile for betabin function

Conrad.hg19.common.CNVs

Conrad et al common CNVs

CallCNVs

Call CNV data from an ExomeDepth object.

count.everted.reads

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

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

ExomeCount

Example dataset for ExomeDepth

exons.hg19.X

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

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

getBamCounts

Get count data for multiple exomes

exons.hg19

Positions of exons on build hg19 of the human genome