est_ptr_on

Requires a minimum of 2 * num_subsets contigs/samples

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

est_ptr_on function

<dl><dt>X</dt>
<dd>cov3 dataframe</dd>
<dt>subset_on</dt>
<dd>either "contig" or "sample"</dd>
<dt>max_attempts</dt>
<dd>max number of attempts to find a valid ptr estimate</dd>
<dt>num_subsets</dt>
<dd>number of subsets to split contigs/samples into</dd>
<dt>cor_cutoff</dt>
<dd>minimum correlation coefficient to accept PTR estimate</dd></dl>

Arguments

Tries up to max_attempts times to compare each permutation of removing random
subsets of contigs/samples from X, and returns the PTR estimate if a valid
one comes back from the comparisons — est_ptr_on

<dl>

<dt>X</dt>
<dd>cov3 dataframe</dd>


<dt>subset_on</dt>
<dd>either "contig" or "sample"</dd>


<dt>max_attempts</dt>
<dd>max number of attempts to find a valid ptr estimate</dd>


<dt>num_subsets</dt>
<dd>number of subsets to split contigs/samples into</dd>


<dt>cor_cutoff</dt>
<dd>minimum correlation coefficient to accept PTR estimate</dd>

</dl>

Tries up to max_attempts times to compare each permutation of removing random
subsets of contigs/samples from X, and returns the PTR estimate if a valid
one comes back from the comparisons

est_ptr_on: Tries up to max_attempts times to compare each permutation of removing random subsets of contigs/samples from X, and returns the PTR estimate if a valid one comes back from the comparisons

Description

Usage

Value

Arguments

Examples