d_left_join

This function joins two tables based on a distance metric of one or more columns. It gives the same results that the <code>distance_left_join</code> function of the <code>fuzzyjoin</code> R package, but its execution time is faster. It is used to match mass spectra to short-listed mass-to-charge values in <code>PredictLogReg</code> and <code>PredictFastClass</code> functions.

Functions to classify mass spectra in known categories and to determine discriminant mass-to-charge values (m/z). Includes easy-to-use preprocessing pipelines for Matrix Assisted Laser Desorption Ionisation - Time Of Flight Mass Spectrometry (MALDI-TOF) mass spectra, methods to select discriminant m/z from labelled libraries, and tools to predict categories (species, phenotypes, etc.) from selected features. Also provides utilities to build design matrices from peak intensities and labels. While this package was developed with the aim of identifying very similar species or phenotypes of bacteria from MALDI-TOF MS, the functions of this package can also be used to classify other categories associated to mass spectra; or from mass spectra obtained with other mass spectrometry techniques. Parallelized processing and optional C++-accelerated functions are available (notably to deal with large datasets) from version 0.5.0. If you use this package in your research, please cite the associated publication (<doi:10.1016/j.eswa.2025.128796>). For a comprehensive guide, additional applications, and detailed examples, see <https://github.com/agodmer/MSclassifR_examples>.

Alexandre Godmer

MSclassifR

Automated Classification of Mass Spectra

Quentin Giai Gianetto

Karen Druart

d_left_join function

<dl> <dt>x</dt>
<dd>A <code>data.frame</code> object.</dd>
 <dt>y</dt>
<dd>A <code>data.frame</code> object.</dd>
 <dt>by</dt>
<dd>Columns by which to join the two tables. <code>NULL</code> by default (tables are joined by matching the common column names that appear in both datasets x and y).</dd>
 <dt>method</dt>
<dd>Method to use for computing distance, either "euclidean" (default) or "manhattan".</dd>
 <dt>max_dist</dt>
<dd>A <code>numeric</code> value indicating the maximum distance to use for joining. 1 by default.</dd>
 <dt>distance_col</dt>
<dd>A <code>character</code> that specifies the name of a new column to be added to the output, which will contain the calculated distances between both tables. If NULL, no column is added (default).</dd></dl>

Arguments

Function joining two tables based not on exact matches — d_left_join

<dl>

 <dt>x</dt>
<dd>A <code>data.frame</code> object.</dd>


 <dt>y</dt>
<dd>A <code>data.frame</code> object.</dd>


 <dt>by</dt>
<dd>Columns by which to join the two tables. <code>NULL</code> by default (tables are joined by matching the common column names that appear in both datasets x and y).</dd>


 <dt>method</dt>
<dd>Method to use for computing distance, either "euclidean" (default) or "manhattan".</dd>


 <dt>max_dist</dt>
<dd>A <code>numeric</code> value indicating the maximum distance to use for joining. 1 by default.</dd>


 <dt>distance_col</dt>
<dd>A <code>character</code> that specifies the name of a new column to be added to the output, which will contain the calculated distances between both tables. If NULL, no column is added (default).</dd>

</dl>

d_left_join: Function joining two tables based not on exact matches

Description

Usage

Value

Arguments