pl_gen_uptake

A protocol that facilitates the processing and analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data using p-value statistics and Critical Interval analysis.
It provides a pipeline for analyzing data from 'HDXExaminer' (Sierra Analytics, Trajan Scientific),
automating matching and comparison of protein states through Welch's T-test and the Critical Interval statistical framework.
Additionally, it simplifies data export, generates 'PyMol' scripts, and ensures calculations meet publication standards.
'HDXBoxeR' assists in various aspects of hydrogen-deuterium exchange data analysis, including reprocessing data, calculating parameters, identifying significant peptides,
generating plots, and facilitating comparison between protein states.
For details check papers by Hageman and Weis (2019) <doi:10.1021/acs.analchem.9b01325>
and Masson et al. (2019) <doi:10.1038/s41592-019-0459-y>.
'HDXBoxeR' citation: Janowska et al. (2024) <doi:10.1093/bioinformatics/btae479>.

Maria K. Janowska

HDXBoxeR

Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

Katherine Reiter

Pearl Magala

Miklos Guttman

Rachel E. Klevit

pl_gen_uptake function

<dl><dt>df</dt>
<dd>dataframe</dd>
<dt>timepoints</dt>
<dd>deuteration times used</dd>
<dt>ddlab</dt>
<dd>label</dd>
<dt>...</dt>
<dd>other</dd></dl>

Arguments

Prepares the plot window for the woods functions — pl_gen_uptake

<dl>

<dt>df</dt>
<dd>dataframe</dd>


<dt>timepoints</dt>
<dd>deuteration times used</dd>


<dt>ddlab</dt>
<dd>label</dd>


<dt>...</dt>
<dd>other</dd>

</dl>

Prepares the plot window for the woods functions

pl_gen_uptake: Prepares the plot window for the woods functions

Description

Usage

Value

Arguments