appearance_to_binary

This function transforms the counts of amino acids to a -1, 0, 1 matrix
based on a probability of appearance of each peptide in each position.

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

appearance_to_binary function

<dl><dt>x</dt>
<dd>A data frame containing peptide sequences.</dd>
<dt>threshold</dt>
<dd>The probability threshold to determine the transformation.</dd>
<dt>group</dt>
<dd>A character string indicating which part of the data to consider. Either 'Best' or 'Worst'.</dd>
<dt>percentage</dt>
<dd>The percentage of the data to consider, if group is specified.</dd></dl>

Arguments

Transform Amino Acid Appearance Probability into -1, 0, or 1 — appearance_to_binary

<dl>

<dt>x</dt>
<dd>A data frame containing peptide sequences.</dd>


<dt>threshold</dt>
<dd>The probability threshold to determine the transformation.</dd>


<dt>group</dt>
<dd>A character string indicating which part of the data to consider. Either 'Best' or 'Worst'.</dd>


<dt>percentage</dt>
<dd>The percentage of the data to consider, if group is specified.</dd>

</dl>

appearance_to_binary: Transform Amino Acid Appearance Probability into -1, 0, or 1

Description

Usage

Value

Arguments

Examples