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 |
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 |
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 |
phiX | Example phiX data |
pi | Example prior |
plot.deepSNV | Scatter plot of relative nucleotide frequencies. |
RCC | Example RCC data |
repeatMask | Mask homopolymeric repeats. |
repeatMask-method | Mask homopolymeric repeats. |
RF | Relative frequencies. |
shearwater | Bayesian beta-binomal test, codename shearwater |
show | Show method for deepSNV objects |
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. |