manhattanPlot

An <code><a rd-options="" href="/link/deepSNV?package=deepSNV&version=1.18.3" data-mini-rdoc="deepSNV::deepSNV">deepSNV</a></code> object.

An optional vector of colors for the nucleotides.


This functions performs a Manhattan plot of the p-values of a deepSNV test against the position


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.

manhattanPlot function

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

This functions performs a Manhattan plot of the p-values of a deepSNV test against the position

manhattanPlot: Manhattan plot.

Description

Usage

Arguments

Value

Examples