histWSAF

Produce histogram of the allele frequency within sample.

Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
(MCMC) approaches, and builds a generic framework that allows haplotype searches
in a multiple infection setting. This package is primarily developed as part of
the Pf3k project, which is a global collaboration using the latest
sequencing technologies to provide a high-resolution view of natural variation
in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
patient blood sample, which often contains more than one parasite strain, with
unknown proportions. This package is used for deconvoluting mixed haplotypes,
and reporting the mixture proportions from each sample.

Joe Zhu

DEploid

Deconvolute Mixed Genomes with Unknown Proportions

Jacob Almagro-Garcia

Gil McVean

University of Oxford 

Yinghan Liu

CodeCogs Zyba Ltd

Deepak Bandyopadhyay

Lutz Kettner

histWSAF function

<dl><dt>obsWSAF</dt>
<dd>Observed allele frequency within sample</dd>
<dt>exclusive</dt>
<dd>When TRUE 0 &lt; WSAF &lt; 1; otherwise 0 &lt;= WSAF &lt;= 1.</dd>
<dt>title</dt>
<dd>Histogram title</dd>
<dt>cex.lab</dt>
<dd>Label size.</dd>
<dt>cex.main</dt>
<dd>Title size.</dd>
<dt>cex.axis</dt>
<dd>Axis text size.</dd></dl>

Arguments

WSAF histogram — histWSAF

<dl>

<dt>obsWSAF</dt>
<dd>Observed allele frequency within sample</dd>


<dt>exclusive</dt>
<dd>When TRUE 0 &lt; WSAF &lt; 1; otherwise 0 &lt;= WSAF &lt;= 1.</dd>


<dt>title</dt>
<dd>Histogram title</dd>


<dt>cex.lab</dt>
<dd>Label size.</dd>


<dt>cex.main</dt>
<dd>Title size.</dd>


<dt>cex.axis</dt>
<dd>Axis text size.</dd>

</dl>

histWSAF: WSAF histogram

Description

Usage

Value

Arguments

Examples