Calls Copy Number Variants from Targeted Sequence Data


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Documentation for package ‘ExomeDepth’ version 1.1.8

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ExomeDepth-package Read depth based CNV calls for exome DNA sequence data
AddAnnotations-method Class 'ExomeDepth'
AnnotateExtra Add annotations to a ExomeDepth object
AnnotateExtra-method Additional annotations for ExomeDepth objects
AnnotateExtra-methods Additional annotations for ExomeDepth objects
CallCNVs Call CNV data from an ExomeDepth object.
CallCNVs-method Class 'ExomeDepth'
Conrad.hg19.common.CNVs Conrad et al common CNVs
count.everted.reads Count the number of everted reads for a set of BAM files.
countBam.everted Counts everted reads from a single BAM file
countBamInGRanges.exomeDepth Compute read count data from BAM files.
ExomeCount Example dataset for ExomeDepth
ExomeDepth Read depth based CNV calls for exome DNA sequence data
ExomeDepth-class Class 'ExomeDepth'
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
genes.hg19 Positions of genes on build hg19 of the human genome
get.power.betabinom Estimate the power to compare two beta-binomial distributions.
getBamCounts Get count data for multiple exomes
initialize-method ~~ Methods for Function 'initialize' ~~
initialize-methods ~~ Methods for Function 'initialize' ~~
plot-method Plotting function for ExomeDepth objects
plot-methods Plotting function for ExomeDepth objects
plot.ExomeDepth Plotting function for ExomeDepth objects
qbetabinom Quantile for betabin function
qbetabinom.ab Quantile function for the beta-binomial distribution
select.reference.set Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.
show-method ~~ Methods for Function 'show' ~~
show-methods ~~ Methods for Function 'show' ~~
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.
TestCNV-method Class 'ExomeDepth'
viterbi.hmm Computes the Viterbi path for a hidden markov model