Detection of subclonal SNVs in deep sequencing data.

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Documentation for package ‘deepSNV’ version 1.51.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

deepSNV-package	Detection of subclonal SNVs in deep sequencing experiments
bam2R	Read nucleotide counts from a .bam file
bbb	Bayesian beta-binomal test, codename shearwater
betabinLRT	ShearwaterML
bf2Vcf	Function to create a 'VCF' object with variant calls from an array of Bayes factors.
consensusSequence	Calculate the consensus sequence.
consensusSequence-method	Calculate the consensus sequence.
control	Get control counts
control-method	Get control counts
coordinates	Get coordinates
coordinates-method	Get coordinates
counts	Example count table
dbetabinom	Beta-binomial probability distribution
deepSNV	Test two matched deep sequencing experiments for low-frequency SNVs.
deepSNV-class	deepSNV class.
deepSNV-method	Test two matched deep sequencing experiments for low-frequency SNVs.
estimateDirichlet	Learn a base-specific Dirichlet prior.
estimateDirichlet-method	Learn a base-specific Dirichlet prior.
estimateDispersion	Estimate the Dispersion factor in a beta-binomial model.
estimateDispersion-method	Estimate the Dispersion factor in a beta-binomial model.
estimateRho	Helper function for estimating the dispersion factor rho
Extract	Subsetting for deepSNV objects.
HIVmix	Example .bam data and true SNVs.
loadAllData	Function to load all data from a list of bam files
makePrior	Compute a prior from a COSMIC VCF object
manhattanPlot	Manhattan plot.
mcChunk	Little helper function to split the count objects into a smaller digestible chunks and run function FUN on each subset
normalize	Normalize nucleotide counts.
normalize-method	Normalize nucleotide counts.
p.combine	Combine two p-values
p.val	Get p-values
p.val-method	Get p-values
pbetabinom	Cumulative beta-binomial probability distribution
phiX	Example phiX data
pi	Example prior
plot.deepSNV	Scatter plot of relative nucleotide frequencies.
qvals2Vcf	Function to create a 'VCF' object with variant calls from an array of q-values.
RCC	Example RCC data
repeatMask	Mask homopolymeric repeats.
repeatMask-method	Mask homopolymeric repeats.
RF	Relative frequencies.
shearwater	Bayesian beta-binomal test, codename shearwater
show-method	Show method for deepSNV objects
summary	Summary of a deepSNV object
summary-method	Summary of a deepSNV object
test	Get test counts
test-method	Get test counts
trueSNVs	Example .bam data and true SNVs.
[-method	Subsetting for deepSNV objects.