Man pages for ExomeDepth
Calls Copy Number Variants from Targeted Sequence Data

AnnotateExtra-ExomeDepth-methodAnnotateExtra
CallCNVs-ExomeDepth-methodCallCNVs
C_hmmC_hmm
Conrad.hg19.common.CNVsConrad et al common CNVs
countBam.evertedCounts everted reads from a single BAM file
countBamInGRanges.exomeDepthCompute read count data from BAM files.
count.everted.readsCount the number of everted reads for a set of BAM files.
ExomeCountExample dataset for ExomeDepth
ExomeDepth-classClass 'ExomeDepth'
exons.hg19Positions of exons on build hg19 of the human genome
exons.hg19.XPositions of exons on build hg19 of the human genome and on...
genes.hg19Positions of genes on build hg19 of the human genome
getBamCountsGet count data for multiple exomes
get_loglike_matrixget_loglike_matrix
get.power.betabinomEstimate the power to compare two beta-binomial...
initialize-ExomeDepth-methodExomeDepth initialization tool
plot-methodsPlotting function for ExomeDepth objects
qbetabinomQuantile for betabin function
qbetabinom.abQuantile function for the beta-binomial distribution
select.reference.setCombine multiple samples to optimize the reference set in...
somatic.CNV.callsomatic.CNV.call
TestCNV-ExomeDepth-methodTestCNV
viterbi.hmmComputes the Viterbi path for a hidden markov model
ExomeDepth documentation built on Jan. 9, 2020, 1:09 a.m.