Package: HDXBoxeR 0.0.2

HDXBoxeR: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

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>.

Authors:Maria K. Janowska [aut, cre], Katherine Reiter [ctb], Pearl Magala [ctb], Miklos Guttman [ctb], Rachel E. Klevit [ctb]

HDXBoxeR_0.0.2.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HDXBoxeR/json (API)

# Install 'HDXBoxeR' in R:

install.packages('HDXBoxeR', repos = c('https://mkajano.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mkajano/hdxboxer/issues

On CRAN:

4.00 score 2 stars 4 scripts 261 downloads 111 exports 22 dependencies

Last updated from:63fdd47db2. Checks:2 NOTE, 7 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	129
source / vignettes	OK	271
linux-release	OK	137
macos-release	OK	150
macos-oldrel	OK	161
windows-devel	NOTE	129
windows-release	OK	100
windows-oldrel	OK	88
wasm-release	OK	115

Exports:all_summary arg_df arg_UN_FD arguments_call1 arguments_call2 arguments_call3 av_tc av_tp ave_timepoint average_timecourse backHX_calculations boxplot_tp CI_2pts CI_single CI_tc CI_tp color_ranges_Blue_Red_heat_map color_ranges_Spectral coverage_residue deuteration_woods_timecourse deuteration_woods_timepoints dif_ave dif_tp dif_tp_proc duplicate_sets extreme_input_gap extreme_input_undeut general_info getCoords1 heat_map_tc heat_map_tp heat_map_tp_maxuptake heat_map_tp_maxuptake_proc heat_map_tp_proc lab_dif lab_dif_proc lab_vol legend_heat_map legend_heat_map_tc legend_heat_map_timecourse legend_heat_map_tp legend_heat_map_tp_proc legend_nm_bottom legend_raw_ave legend_raw_ave_proc legend_raw_ave_tc legend_sig_peptides legend_states_PerD_bottom legend_tc_bottom nb_exch_deut nm_states output_FD output_FD_proc output_prep output_tc output_tp output_UD output_UD_proc pallette_legend pallette_ll peptide_pv_tp peptide_pv_tp_proc pl_gen_ch2 pl_gen_uptake plot_heat_map_max_uptake_tp plot_heat_map_max_uptake_tp_proc plot_heat_map_tc plot_heat_map_tp plot_heat_map_tp_proc plot_peptide_sig_tp plot_peptide_sig_tp_proc plots_av_tcourse plots_av_tp plots_av_tp_proc plots_diff_tp plots_diff_tp_proc plots_vol_tp ppar ppar_bottom_legend ppar_wider pparLM prep_timecourse_plot_ave prep_timecourse_plot_sd pv_timecourse pv_timepoint pymol_script_average_residue pymol_script_significant_peptide pymol_script_significant_peptide_proc pymol_script_significant_residue pymol_script_significant_residue_proc pymol_str qpcr.cbind.na ranges_function ranges_function_tc rbind_na reset_par robot_2states_indexes robot_indexes robot_indexes_df robot_plot_All sd_timecourse sd_timecourse_proc sd_timepoint select_indices significant_peptide_uptake summary_sd_CI uptake_plots verbose_timecourse_output verbose_timepoint_output vol_tp woods_CI_plot

Dependencies:cli cpp11 dplyr generics glue lifecycle magrittr pillar pkgconfig purrr R6 RColorBrewer rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr wrapr

HDXBoxeR

Rendered fromHDXBoxeR.Rmdusingknitr::rmarkdown

Last update: 2024-08-14
Started: 2021-03-03

Help page	Topics
Returns full summary table.	all_summary
Returns initially processed data.frame from the export from the HDXExaminer	arg_df
Returns initially processed data.frame from the export from the HDXExaminer	arg_UN_FD
Returns default arguments for the output_tp functions. States	arguments_call1
Returns default arguments for the output_tp functions. Deut.Time	arguments_call2
Returns default arguments for the output_tp functions. # replicates	arguments_call3
Preparatory function for average plot for timecourses	av_tc
Preparatory function for average plot	av_tp
Returns average value for either uptake of procent data.	ave_timepoint
Calculates average for time course data.	average_timecourse
Summary of backexchange summary	backHX_calculations
Plots boxplots for all the averages in the set	boxplot_tp
Global confidence interval treshold from experimental standard deviation for 2 samples.	CI_2pts
Global confidence interval treshold from experimental standard deviation for 1 sample	CI_single
Critial interval calculation two sets of timecourses	CI_tc
Global confidence interval treshold from experimental standard deviation	CI_tp
Returns color pallete from red to blue with number of colors for defined ranges	color_ranges_Blue_Red_heat_map
Returns Spectral pallette with colors matching defined ranges	color_ranges_Spectral
Returns coverage per residue	coverage_residue
Return woods plots for the timecourse	deuteration_woods_timecourse
Return woods plots for the timepoints	deuteration_woods_timepoints
Returns data frame with difference of averages between State1 and other states provided.	dif_ave
Preparatory function for difference plot	dif_tp
Preparatory function for difference plot	dif_tp_proc
Duplicate set function	duplicate_sets
Makes input for Extreme for bimodal analysis.	extreme_input_gap
Makes input for Extreme for bimodal analysis.	extreme_input_undeut
Provides summary table for all data.sets.	general_info
function from plotfunctions package	getCoords1
Plots heat maps for time courses.	heat_map_tc
Preparatory function for heat map	heat_map_tp
Preparatory function for heat map of maximum uptake per residue.	heat_map_tp_maxuptake
Preparatory function for heat map of maximum procent deuteration per residue.	heat_map_tp_maxuptake_proc
Preparatory function for heat map for procent deuteration	heat_map_tp_proc
Checks for NaN is data.frame	is.nan.data.frame
Legend for difference in averages plot.	lab_dif
Preparatory function for difference plot for procent deuteration	lab_dif_proc
Preparatory function for volcano plot legends	lab_vol
Legend for the heatmaps prep function.	legend_heat_map
Legend for the heatmaps for timecourses.	legend_heat_map_tc
Legend for the heatmaps prep function for timecourses.	legend_heat_map_timecourse
Legend for the heatmaps.Extracts names from data.frame	legend_heat_map_tp
Legend for the heatmaps percent.Extracts names from data.frame	legend_heat_map_tp_proc
Legend, bottom of the plots	legend_nm_bottom
Legend for average plot.	legend_raw_ave
Preparatory function to draw legends for average procent	legend_raw_ave_proc
Legend for average deuteration plot for timecourse.	legend_raw_ave_tc
Legend for the significant peptides	legend_sig_peptides
Legend, bottom of the plots	legend_states_PerD_bottom
Preparatory function returns legends for the timecourses.	legend_tc_bottom
Number of exchangeable protons	nb_exch_deut
Lists names of states in data sets	nm_states
Prepares output for HDX-MS Full deuteration data	output_FD
Prepares output for HDX-MS Full deuteration data for procent deuteration.	output_FD_proc
Prepares output with HDX-MS data for publications	output_prep
Prepares output for HDX-MS for the deuteration uptake or percent deuteration for the time courses.	output_tc
Prepares output for HDX-MS for the deuteration uptake or percent deuteration for the time points.	output_tp
Prepares output for HDX-MS Undeuterated sample data.	output_UD
Prepares output for HDX-MS Undeuterated data for procent deuteration.	output_UD_proc
Color scheme using heatmap. Legend Extracts names from data.frame	pallette_legend
Color scheme using heatmap. Legend extracts names from data frame	pallette_ll
Preparatory function for significant peptide plots	peptide_pv_tp
Preparatory function for showing peptides with significant differences between sets.	peptide_pv_tp_proc
Prepares the plot window for the woods functions	pl_gen_ch2
Prepares the plot window for the woods functions	pl_gen_uptake
Plots heat maps for maximum uptake per residue.	plot_heat_map_max_uptake_tp
Plots heat maps for maximum procent deuteration per residue.	plot_heat_map_max_uptake_tp_proc
Plots heat maps for time courses.	plot_heat_map_tc
Plots heat maps for significant peptides.	plot_heat_map_tp
Plots heat maps for significant peptides.	plot_heat_map_tp_proc
Significant peptide plots.	plot_peptide_sig_tp
Draws peptides with significant difefrences between sets.	plot_peptide_sig_tp_proc
Generates average deuteration plot for the time-course.	plots_av_tcourse
Returns average deuteration plot for timepoints in the data frame	plots_av_tp
Returns average procent deuteration plot for time points	plots_av_tp_proc
Returns difference in average plot for timepoints in the data frame	plots_diff_tp
Returns difference in average procent deuteration plot for timepoints in the data frame	plots_diff_tp_proc
Returns volcano plots for timepoints in the data frame	plots_vol_tp
Preparation of figure window.	ppar
Preparation of figure window with area for figure at the bottom.	ppar_bottom_legend
Preparation of figure window with more area on west side of plot.	ppar_wider
Preparation of figure window. small margins	pparLM
Prepares function for plotting averages in timecourse	prep_timecourse_plot_ave
Prepares function for Critical interval for timecourses	prep_timecourse_plot_sd
pvalue calculation between two sets of the data at certain timepoint	pv_timecourse
Calculation of pvalue between first protein state and any other state from all_states file	pv_timepoint
Writes a text files with pymol scripts to list significant residues.	pymol_script_average_residue
Writes a text files with pymol scripts to list significant peptides	pymol_script_significant_peptide
Writes a text files with pymol scripts to list significant peptides	pymol_script_significant_peptide_proc
Writes a text files with pymol scripts to list significant residues.	pymol_script_significant_residue
Writes a text files with pymol scripts to list significant residues.	pymol_script_significant_residue_proc
Preparatory function writing pymol scripts	pymol_str
Hidden function from qpcR package, typical usage as qpcR:::cbind.na	qpcr.cbind.na
Gives ranges for the averages	ranges_function
Gives ranges for the averages for time course analysis	ranges_function_tc
bind non equal row	rbind_na
Reset plotting window parameters to default	reset_par
Returns a robot plot for selected peptides for 2 protein states.	robot_2states_indexes
Returns indexes for peptides with significant difference between two sets	robot_indexes
Returns dataframe with peptides which exhibit significant difference between two sets	robot_indexes_df
Returns a robot plot for comparisons of the timepoints samples	robot_plot_All
Returns standard deviation for uptake data for timecourses.	sd_timecourse
Returns standard deviation for percent deuteration data for timecourses.	sd_timecourse_proc
Returns standard deviation for dataframe.	sd_timepoint
Allows for selecting some peptide from input data	select_indices
Function returns which peptides are significantly based of pv_cutoff and Critial interval	significant_peptide_uptake
Provides summary table with Critical interval and standard deviation within the set.	summary_sd_CI
Uptake plots	uptake_plots
Returns csv with averages from analysis for procent deuteration file, standard deviation for time courses.	verbose_timecourse_output
Returns csv with averages from analysis for uptake file, standard deviation, p-values.	verbose_timepoint_output
Preparatory function for volcano plot	vol_tp
Returns a woods plot for comparisons of the timepoints samples	woods_CI_plot

Package: HDXBoxeR 0.0.2

HDXBoxeR: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

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