Man pages for deepSNV
Detection of subclonal SNVs in deep sequencing data.

bam2RRead nucleotide counts from a .bam file
betabinLRTShearwaterML
bf2VcfFunction to create a 'VCF' object with variant calls from an...
consensusSequence-methodsCalculate the consensus sequence.
control-methodsGet control counts
coordinates-methodsGet coordinates
countsExample count table
dbetabinomBeta-binomial probability distribution
deepSNV-classdeepSNV class.
deepSNV-methodsTest two matched deep sequencing experiments for...
deepSNV-packageDetection of subclonal SNVs in deep sequencing experiments
estimateDirichlet-methodsLearn a base-specific Dirichlet prior.
estimateDispersion-methodsEstimate the Dispersion factor in a beta-binomial model.
estimateRhoHelper function for estimating the dispersion factor rho
Extract-methodsSubsetting for deepSNV objects.
loadAllDataFunction to load all data from a list of bam files
makePriorCompute a prior from a COSMIC VCF object
manhattanPlotManhattan plot.
mcChunkLittle helper function to split the count objects into a...
normalize-methodsNormalize nucleotide counts.
pbetabinomCumulative beta-binomial probability distribution
p.combineCombine two p-values
phiXExample phiX data
piExample prior
plot.deepSNVScatter plot of relative nucleotide frequencies.
p.val-methodsGet p-values
qvals2VcfFunction to create a 'VCF' object with variant calls from an...
RCCExample RCC data
repeatMask-methodsMask homopolymeric repeats.
RFRelative frequencies.
shearwaterBayesian beta-binomal test, codename shearwater
show-deepSNV-methodShow method for deepSNV objects
summary-methodsSummary of a deepSNV object
test-methodsGet test counts
trueSNVsExample .bam data and true SNVs.
deepSNV documentation built on May 31, 2017, 11:17 a.m.