Test for subclonal SNVs in deep sequencing experiments.


[Up] [Top]

Documentation for package ‘deepSNV’ version 1.2.3

Help Pages

deepSNV-package Estimation of single nucleotide variants from paired deep sequencing experiments
bam2R Read nucleotide counts...
consensusSequence Calculate the consensus sequence.
consensusSequence-method Calculate the consensus sequence.
consensusSequence-methods Calculate the consensus sequence.
control Get control counts...
control-method Get control counts...
control-methods Get control counts...
coordinates Get coordinates...
coordinates-method Get coordinates...
coordinates-methods 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.
deepSNV-methods 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.
estimateDirichlet-methods 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.
estimateDispersion-methods Estimate the Dispersion factor in a beta-binomial model.
HIVmix Example...
manhattanPlot Manhattan plot.
normalize Normalize nucleotide counts.
normalize-method Normalize nucleotide counts.
normalize-methods Normalize nucleotide counts.
p.combine Combine two p-values...
p.val Get p-values...
p.val-method Get p-values...
p.val-methods Get p-values...
phiX Example phiX data...
plot.deepSNV Scatter plot of relative nucleotide frequencies.
RCC Example RCC data...
repeatMask Mask homopolymeric repeats.
repeatMask-method Mask homopolymeric repeats.
repeatMask-methods Mask homopolymeric repeats.
RF Relative frequencies.
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...
summary-methods Summary of a deepSNV object...
test Get test counts...
test-method Get test counts...
test-methods Get test counts...
trueSNVs Example...
[ Subsetting for deepSNV objects.
[-method Subsetting for deepSNV objects.