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ExomeDepth (version 1.1.15)

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

117

Version

1.1.15

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

January 9th, 2020

Functions in ExomeDepth (1.1.15)

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

plot-methods

Plotting function for ExomeDepth objects

initialize,ExomeDepth-method

ExomeDepth initialization tool

countBam.everted

Counts everted reads from a single BAM file

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

genes.hg19

Positions of genes on build hg19 of the human genome

qbetabinom

Quantile for betabin function

getBamCounts

Get count data for multiple exomes

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

get_loglike_matrix

qbetabinom.ab

Quantile function for the beta-binomial distribution

viterbi.hmm

Computes the Viterbi path for a hidden markov model

select.reference.set

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

somatic.CNV.call

CallCNVs,ExomeDepth-method

CallCNVs

Conrad.hg19.common.CNVs

Conrad et al common CNVs

TestCNV,ExomeDepth-method

TestCNV

AnnotateExtra,ExomeDepth-method

AnnotateExtra

C_hmm

count.everted.reads

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

ExomeCount

Example dataset for ExomeDepth

ExomeDepth-class

Class ExomeDepth