control

control,deepSNV-method

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

deepSNV

Logical. If true the sum of both strands is returned

total

Additional param passed to specific methods


Convenience function to obtain the control counts from a deepSNV object.


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

Detection of subclonal SNVs in deep sequencing data.

control function

a <code><a href="deepSNV-class" rd-options="">deepSNV-class</a></code> object

Convenience function to obtain the control counts from a deepSNV object.

control: Get control counts

Description

Usage

Arguments

Value

Examples