plots_vol_tp

Returns volcano plots for each peptide. Critical interval is calculated according to #' Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach
Tyler S. Hageman and David D. Weis
Analytical Chemistry 2019 91 (13), 8008-8016 DOI: 10.1021/acs.analchem.9b01325
calculations for alpha 0.99
pvalues calculated using Welch t-test.

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

plots_vol_tp function

<dl><dt>df</dt>
<dd>output from functions output_tp</dd>
<dt>replicates</dt>
<dd>number of replicates in set as default set to 3.</dd>
<dt>pv_cutoff</dt>
<dd>p-value cutoff here set up to 0.01</dd>
<dt>cola</dt>
<dd>color pallette for different Protein States. As default Paired pallette from color.Brewer is used.</dd></dl>

Arguments

Returns volcano plots for timepoints in the data frame — plots_vol_tp

<dl>

<dt>df</dt>
<dd>output from functions output_tp</dd>


<dt>replicates</dt>
<dd>number of replicates in set as default set to 3.</dd>


<dt>pv_cutoff</dt>
<dd>p-value cutoff here set up to 0.01</dd>


<dt>cola</dt>
<dd>color pallette for different Protein States. As default Paired pallette from color.Brewer is used.</dd>

</dl>

plots_vol_tp: Returns volcano plots for timepoints in the data frame

Description

Usage

Value

Arguments

Examples