extract_features_QSAR

This function extracts various Quantitative Structure-Activity Relationship (QSAR) features
from peptide sequences. The extraction is based on a variety of amino acid properties
and functions from the "Peptides" package (https://github.com/dosorio/Peptides/).

This toolkit is designed for manipulation and analysis of peptides. It provides functionalities to assist researchers in peptide engineering and proteomics. Users can manipulate peptides by adding amino acids at every position, count occurrences of each amino acid at each position, and transform amino acid counts based on probabilities. The package offers functionalities to select the best versus the worst peptides and analyze these peptides, which includes counting specific residues, reducing peptide sequences, extracting features through One Hot Encoding (OHE), and utilizing Quantitative Structure-Activity Relationship (QSAR) properties (based in the package 'Peptides' by Osorio et al. (2015) <doi:10.32614/RJ-2015-001>). This package is intended for both researchers and bioinformatics enthusiasts working on peptide-based projects, especially for their use with machine learning.

Josep-Ramon Codina

peptoolkit

A Toolkit for Using Peptide Sequences in Machine Learning

extract_features_QSAR function

<dl><dt>n</dt>
<dd>The length of the peptide sequences.Must be more than 2.</dd>
<dt>pH</dt>
<dd>The pH used for calculating charge (default is 7.4).</dd>
<dt>custom.list</dt>
<dd>A boolean indicating if a custom peptide list is provided (default is FALSE).</dd>
<dt>PeList</dt>
<dd>The custom list of peptides (required if custom.list is TRUE).</dd>
<dt>rem.cys</dt>
<dd>A boolean indicating if sequences with Cys should be removed (default is FALSE).</dd>
<dt>rem.met</dt>
<dd>A boolean indicating if sequences with Met should be removed (default is FALSE).</dd>
<dt>rem.sali</dt>
<dd>A boolean indicating if sequences with 2 or more small aliphatic amino acids should be removed (default is FALSE).</dd>
<dt>norm</dt>
<dd>A boolean indicating if the data should be normalized (default is FALSE).</dd></dl>

Arguments

Extract QSAR Features from Peptide Sequences — extract_features_QSAR

<dl>

<dt>n</dt>
<dd>The length of the peptide sequences.Must be more than 2.</dd>


<dt>pH</dt>
<dd>The pH used for calculating charge (default is 7.4).</dd>


<dt>custom.list</dt>
<dd>A boolean indicating if a custom peptide list is provided (default is FALSE).</dd>


<dt>PeList</dt>
<dd>The custom list of peptides (required if custom.list is TRUE).</dd>


<dt>rem.cys</dt>
<dd>A boolean indicating if sequences with Cys should be removed (default is FALSE).</dd>


<dt>rem.met</dt>
<dd>A boolean indicating if sequences with Met should be removed (default is FALSE).</dd>


<dt>rem.sali</dt>
<dd>A boolean indicating if sequences with 2 or more small aliphatic amino acids should be removed (default is FALSE).</dd>


<dt>norm</dt>
<dd>A boolean indicating if the data should be normalized (default is FALSE).</dd>

</dl>

extract_features_QSAR: Extract QSAR Features from Peptide Sequences

Description

Usage

Value

Arguments

Examples