| 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. |