unreliable_regions

A data frame of unmappable regions and regions of CG% and A% over 60% and 45%
respectively for the virus segments. It is worth to note that if a
virus segment does not have any unreliable regions, that virus segment is not
shown in this data frame.

datasets

A novel machine learning method for plant viruses diagnostic using
genome sequencing data. This package includes three different machine
learning models, random forest, XGBoost, and elastic net, to train and
predict mapped genome samples. Mappability profile and unreliable regions
are introduced to the algorithm, and users can build a mappability profile
from scratch with functions included in the package. Plotting mapped sample
coverage information is provided.

Xuekui Zhang

iimi

Identifying Infection with Machine Intelligence

Haochen Ning

Ian Boyes

Ibrahim Numanagić

Michael Rott

Li Xing

unreliable_regions function

A data frame of unreliable regions in the run-length encoding format
for virus segments.<dl>
<dt>Start</dt>
<dd>The start position of the region that is considered unreliable</dd><dt>End</dt>
<dd>The end position of the region that is considered unreliable</dd><dt>Virus segment</dt>
<dd>The virus segment ID</dd><dt>Categories</dt>
<dd>The category that this unrelible region belong to, which
are Unmappable regions (host), Unmappable regions (virus), CG% &gt; 60%, A% &gt; 45%</dd><dt>1_4_0</dt>
<dd>The version number of the virus database</dd><dt>1_5_0</dt>
<dd>The version number of the virus database</dd>
</dl>

Format

The unreliable regions of the virus segments — unreliable_regions

A data frame of unreliable regions in the run-length encoding format
for virus segments.<dl>
<dt>Start</dt>
<dd>The start position of the region that is considered unreliable</dd>

<dt>End</dt>
<dd>The end position of the region that is considered unreliable</dd>

<dt>Virus segment</dt>
<dd>The virus segment ID</dd>

<dt>Categories</dt>
<dd>The category that this unrelible region belong to, which
are Unmappable regions (host), Unmappable regions (virus), CG% &gt; 60%, A% &gt; 45%</dd>

<dt>1_4_0</dt>
<dd>The version number of the virus database</dd>

<dt>1_5_0</dt>
<dd>The version number of the virus database</dd>


</dl>

unreliable_regions: The unreliable regions of the virus segments

Description

Usage

Arguments

Format