haplotypePainter

Plot the posterior probabilities of a haplotype given the refernece panel.

'DEploid' (Zhu et.al. 2018 <doi:10.1093/bioinformatics/btx530>)
is designed for deconvoluting mixed genomes with unknown
proportions. Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo
(MCMC) approaches, and builds a generic framework that allows haloptype
searches in a multiple infection setting. This package provides R functions
to support data analysis and results interpretation.

Joe Zhu

DEploid.utils

'DEploid' Data Analysis and Results Interpretation

Jacob Almagro-Garcia

Gil McVean

University of Oxford 

Yinghan Liu

CodeCogs Zyba Ltd

Deepak Bandyopadhyay

Lutz Kettner

haplotypePainter function

<dl><dt>posteriorProbabilities</dt>
<dd>Posterior probabilities matrix with the size of number of loci by the number of reference strain.</dd>
<dt>title</dt>
<dd>Figure title.</dd>
<dt>labelScaling</dt>
<dd>Scaling parameter for plotting.</dd>
<dt>numberOfInbreeding</dt>
<dd>Number of inbreading strains</dd></dl>

Arguments

Painting haplotype according the reference panel — haplotypePainter

<dl>

<dt>posteriorProbabilities</dt>
<dd>Posterior probabilities matrix with the size of number of loci by the number of reference strain.</dd>


<dt>title</dt>
<dd>Figure title.</dd>


<dt>labelScaling</dt>
<dd>Scaling parameter for plotting.</dd>


<dt>numberOfInbreeding</dt>
<dd>Number of inbreading strains</dd>

</dl>

haplotypePainter: Painting haplotype according the reference panel

Description

Usage

Value

Arguments