filter_sample

A function for sample filtration
Input requirements: 1. have values in more than half of the contigs 2. average log2(cov) &gt; 0 in all these contigs

Multi-sample algorithm based on contigs and coverage values, to
infer the relative distances of contigs from the replication origin and to
accurately compare bacterial growth rates between samples. Yuan Gao and
Hongzhe Li (2018) <doi:10.1038/s41592-018-0182-0>.

Charlie Bushman

demic

Dynamic Estimator of Microbial Communities

Yuan Gao

filter_sample function

<dl><dt>Z</dt>
<dd>a matrix</dd>
<dt>avg_cutoff</dt>
<dd>threshold of average</dd>
<dt>cutoff_ratio</dt>
<dd>threshold of ratio</dd></dl>

Arguments

A function for sample filtration
Input requirements: 1. have values in more than half of the contigs 2. average log2(cov) &gt; 0 in all these contigs — filter_sample

<dl>

<dt>Z</dt>
<dd>a matrix</dd>


<dt>avg_cutoff</dt>
<dd>threshold of average</dd>


<dt>cutoff_ratio</dt>
<dd>threshold of ratio</dd>

</dl>

filter_sample: A function for sample filtration Input requirements: 1. have values in more than half of the contigs 2. average log2(cov) > 0 in all these contigs

Description

Usage

Value

Arguments