Man pages for gerstung-lab/deepSNV
Detection of subclonal SNVs in deep sequencing data.
| bam2R | Read nucleotide counts from a .bam file |
| betabinLRT | ShearwaterML |
| bf2Vcf | Function to create a 'VCF' object with variant calls from an... |
| consensusSequence-methods | Calculate the consensus sequence. |
| control-methods | Get control counts |
| coordinates-methods | Get coordinates |
| counts | Example count table |
| dbetabinom | Beta-binomial probability distribution |
| deepSNV-class | deepSNV class. |
| deepSNV-methods | Test two matched deep sequencing experiments for... |
| deepSNV-package | Detection of subclonal SNVs in deep sequencing experiments |
| estimateDirichlet-methods | Learn a base-specific Dirichlet prior. |
| estimateDispersion-methods | Estimate the Dispersion factor in a beta-binomial model. |
| estimateRho | Helper function for estimating the dispersion factor rho |
| Extract-methods | Subsetting for deepSNV objects. |
| 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... |
| normalize-methods | Normalize nucleotide counts. |
| pbetabinom | Cumulative beta-binomial probability distribution |
| p.combine | Combine two p-values |
| phiX | Example phiX data |
| pi | Example prior |
| plot.deepSNV | Scatter plot of relative nucleotide frequencies. |
| p.val-methods | Get p-values |
| qvals2Vcf | Function to create a 'VCF' object with variant calls from an... |
| RCC | Example RCC data |
| repeatMask-methods | Mask homopolymeric repeats. |
| RF | Relative frequencies. |
| shearwater | Bayesian beta-binomal test, codename shearwater |
| show-deepSNV-method | Show method for deepSNV objects |
| summary-methods | Summary of a deepSNV object |
| test-methods | Get test counts |
| trueSNVs | Example .bam data and true SNVs. |
