read_pli

Implements a parsimonious evolutionary model to analyze and
predict gene-functional annotations in phylogenetic trees as described in Vega
Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on
computational efficiency, 'aphylo' makes it possible to estimate pooled
phylogenetic models, including thousands (hundreds) of annotations (trees) in
the same run. The package also provides the tools for visualization of
annotated phylogenies, calculation of posterior probabilities (prediction)
and goodness-of-fit assessment featured in Vega Yon et al. (2021).

George Vega Yon

aphylo

Statistical Inference and Prediction of Annotations in
Phylogenetic Trees

National
Cancer Institute (NCI) 

USC Biostatistics 

read_pli function

<dl><dt>fn</dt>
<dd>Full path to the file</dd>
<dt>dropNAs</dt>
<dd>Logical scalar. When <code>TRUE</code>, the function will discard any
protein that has no annotations.</dd></dl>

Arguments

Read PLI files from SIFTER — read_pli

<dl>

<dt>fn</dt>
<dd>Full path to the file</dd>


<dt>dropNAs</dt>
<dd>Logical scalar. When <code>TRUE</code>, the function will discard any
protein that has no annotations.</dd>

</dl>

read_pli: Read PLI files from SIFTER

Description

Usage

Value

Arguments

See Also