estimateDirichlet

estimateDirichlet,deepSNV-method

estimateDirichlet,matrix-method

Either a matrix with nucleotide counts or a <code><a rd-options="" href="/link/deepSNV-class?package=deepSNV&version=1.18.3" data-mini-rdoc="deepSNV::deepSNV-class">deepSNV-class</a></code> object.

control


The prior learns the parameters of a Dirichlet distribution seperately for each consensus base. The expected value of the Dirichlet distributions
is the base-substitution matrix, where rows correspond to the initial nucleotide and columns to the substituted nucleotide. The absolute values determine
the higher moments of the Dirichlet distributions. After having learned the prior the <code><a rd-options="" href="/link/deepSNV-class?package=deepSNV&version=1.18.3" data-mini-rdoc="deepSNV::deepSNV-class">deepSNV-class</a></code> test is recomputed.


This package provides provides quantitative variant callers for
detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing
experiments. The deepSNV algorithm is used for a comparative setup with a
control experiment of the same loci and uses a beta-binomial model and a
likelihood ratio test to discriminate sequencing errors and subclonal SNVs.
The shearwater algorithm computes a Bayes classifier based on a
beta-binomial model for variant calling with multiple samples for
precisely estimating model parameters such as local error rates and
dispersion and prior knowledge, e.g. from variation data bases such as
COSMIC.

Moritz Gerstung

deepSNV

Detection of subclonal SNVs in deep sequencing data.

estimateDirichlet function

Either a matrix with nucleotide counts or a <code><a href="deepSNV-class" rd-options="">deepSNV-class</a></code> object.

The prior learns the parameters of a Dirichlet distribution seperately for each consensus base. The expected value of the Dirichlet distributions
is the base-substitution matrix, where rows correspond to the initial nucleotide and columns to the substituted nucleotide. The absolute values determine
the higher moments of the Dirichlet distributions. After having learned the prior the <code><a href="deepSNV-class" rd-options="">deepSNV-class</a></code> test is recomputed.

estimateDirichlet: Learn a base-specific Dirichlet prior.

Description

Usage

Arguments

Value

Examples