pipeline

A function representing the pipeline of four steps
including GC bias correction, sample filtration, PCA and contig filtration

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

pipeline function

<dl><dt>Y</dt>
<dd>a matrix of coverages</dd>
<dt>i</dt>
<dd>cutoff of filtering samples changes according to parameter i; i=1, cutoffRatio is 0.5; i=2, cutoffRatio is 1 as contig is clean</dd></dl>

Arguments

A function representing the pipeline of four steps
including GC bias correction, sample filtration, PCA and contig filtration — pipeline

<dl>

<dt>Y</dt>
<dd>a matrix of coverages</dd>


<dt>i</dt>
<dd>cutoff of filtering samples changes according to parameter i; i=1, cutoffRatio is 0.5; i=2, cutoffRatio is 1 as contig is clean</dd>

</dl>

pipeline: A function representing the pipeline of four steps including GC bias correction, sample filtration, PCA and contig filtration

Description

Usage

Value

Arguments