enve.recplot2.ANIr

Estimate the Average Nucleotide Identity from reads (ANIr) from a
recruitment plot.

A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).

Luis M RodriguezR

enveomics.R

Various Utilities for Microbial Genomics and Metagenomics

Luis M. Rodriguez-R

enve.recplot2.ANIr function

<dl><dt>x</dt>
<dd><code>enve.RecPlot2</code> object.</dd>
<dt>range</dt>
<dd>Range of identities to be considered. By default, the full range
is used (note that the upper boundary is <code>Inf</code> and not 100 because
recruitment plots can also be built with bit-scores). To use only
intra-population matches (with identities), use <code>c(95, 100)</code>. To use
only inter-population values, use <code>c(0, 95)</code>.</dd></dl>

Arguments

Author

Enveomics: Recruitment Plot (2) ANI Estimate — enve.recplot2.ANIr

<dl>

<dt>x</dt>
<dd><code>enve.RecPlot2</code> object.</dd>


<dt>range</dt>
<dd>Range of identities to be considered. By default, the full range
is used (note that the upper boundary is <code>Inf</code> and not 100 because
recruitment plots can also be built with bit-scores). To use only
intra-population matches (with identities), use <code>c(95, 100)</code>. To use
only inter-population values, use <code>c(0, 95)</code>.</dd>

</dl>

enve.recplot2.ANIr: Enveomics: Recruitment Plot (2) ANI Estimate

Description

Usage

Value

Arguments

Author