nucleotide_info

A data set containing the GC content and other information about the virus
segments from the official Virtool virus data base (version 1.4.0). The
variables are as follows:

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

nucleotide_info function

A data frame with 7 variables:<dl>
<dt>virus_name</dt>
<dd>The virus name</dd><dt>iso_id</dt>
<dd>The virus isolate ID</dd><dt>seg_id</dt>
<dd>The virus segment ID</dd><dt>A_percent</dt>
<dd>The percentage of A nucleotides in the virus segment</dd><dt>C_percent</dt>
<dd>The percentage of C nucleotides in the virus segment</dd><dt>T_percent</dt>
<dd>The percentage of T nucleotides in the virus segment</dd><dt>GC_percent</dt>
<dd>The percentage of G and C nucleotides in the virus
segment (GC content)</dd><dt>seg_len</dt>
<dd>The length of the virus segment</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

Nucleotide information of virus segments — nucleotide_info

A data frame with 7 variables:<dl>
<dt>virus_name</dt>
<dd>The virus name</dd>

<dt>iso_id</dt>
<dd>The virus isolate ID</dd>

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

<dt>A_percent</dt>
<dd>The percentage of A nucleotides in the virus segment</dd>

<dt>C_percent</dt>
<dd>The percentage of C nucleotides in the virus segment</dd>

<dt>T_percent</dt>
<dd>The percentage of T nucleotides in the virus segment</dd>

<dt>GC_percent</dt>
<dd>The percentage of G and C nucleotides in the virus
segment (GC content)</dd>

<dt>seg_len</dt>
<dd>The length of the virus segment</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>

nucleotide_info: Nucleotide information of virus segments

Description

Usage

Arguments

Format