significant_peptide_uptake

Returns data frame with significant peptides.

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

significant_peptide_uptake function

<dl><dt>df_av</dt>
<dd>data.frame with averages created using ave_timepoint() function</dd>
<dt>pv</dt>
<dd>data.frame with pvalues created using pv_timepoint() function</dd>
<dt>sd</dt>
<dd>data.frame with standard deviations created using sd_timepoint() function</dd>
<dt>pv_cutoff</dt>
<dd>cuttoff for Critical interval. Default=0.01</dd>
<dt>replicates</dt>
<dd>number of replicates as default set to 3.</dd></dl>

Arguments

Function returns which peptides are significantly based of pv_cutoff and Critial interval — significant_peptide_uptake

<dl>

<dt>df_av</dt>
<dd>data.frame with averages created using ave_timepoint() function</dd>


<dt>pv</dt>
<dd>data.frame with pvalues created using pv_timepoint() function</dd>


<dt>sd</dt>
<dd>data.frame with standard deviations created using sd_timepoint() function</dd>


<dt>pv_cutoff</dt>
<dd>cuttoff for Critical interval. Default=0.01</dd>


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

</dl>

significant_peptide_uptake: Function returns which peptides are significantly based of pv_cutoff and Critial interval

Description

Usage

Value

Arguments