select_indices

Function allows for picking indices from the inputs based on:
peptide start or end residue, length, state or timepoint.
If parameters set to NA, condition is skipped.

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

select_indices function

<dl><dt>df</dt>
<dd>input file (output of output_tc or output_tp)</dd>
<dt>start</dt>
<dd>provide number for the staring residue, default NA</dd>
<dt>end</dt>
<dd>provide number for the end residue, default NA</dd>
<dt>length</dt>
<dd>provide max length of the peptide</dd>
<dt>times</dt>
<dd>timepoints, only for the output_tp functions</dd>
<dt>states</dt>
<dd>states, only for the output_tc functions</dd></dl>

Arguments

Allows for selecting some peptide from input data — select_indices

<dl>

<dt>df</dt>
<dd>input file (output of output_tc or output_tp)</dd>


<dt>start</dt>
<dd>provide number for the staring residue, default NA</dd>


<dt>end</dt>
<dd>provide number for the end residue, default NA</dd>


<dt>length</dt>
<dd>provide max length of the peptide</dd>


<dt>times</dt>
<dd>timepoints, only for the output_tp functions</dd>


<dt>states</dt>
<dd>states, only for the output_tc functions</dd>

</dl>

select_indices: Allows for selecting some peptide from input data

Description

Usage

Value

Arguments

Examples