plots_av_tp

Returns plots with average deuteration at each peptide.

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_av_tp function

<dl><dt>df</dt>
<dd>output from functions output_tp or output_tp_proc.</dd>
<dt>replicates</dt>
<dd>number of replicates in set as default set to 3.</dd>
<dt>cola</dt>
<dd>color pallette for different Protein States. As default Paired pallette from color.Brewer is used.</dd></dl>

Arguments

Returns average deuteration plot for timepoints in the data frame — plots_av_tp

<dl>

<dt>df</dt>
<dd>output from functions output_tp or output_tp_proc.</dd>


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


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

</dl>

plots_av_tp: Returns average deuteration plot for timepoints in the data frame

Description

Usage

Value

Arguments

Examples