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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HDXBoxeR.pdf |HDXBoxeR.html✨
HDXBoxeR/json (API)

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

Peer review:

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

On CRAN:

4.70 score 2 stars 3 scripts 181 downloads 111 exports 23 dependencies

Last updated 3 months agofrom:63fdd47db2. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winOKNov 17 2024
R-4.5-linuxOKNov 17 2024
R-4.4-winOKNov 17 2024
R-4.4-macOKNov 17 2024
R-4.3-winOKNov 17 2024
R-4.3-macOKNov 17 2024

Exports:all_summaryarg_dfarg_UN_FDarguments_call1arguments_call2arguments_call3av_tcav_tpave_timepointaverage_timecoursebackHX_calculationsboxplot_tpCI_2ptsCI_singleCI_tcCI_tpcolor_ranges_Blue_Red_heat_mapcolor_ranges_Spectralcoverage_residuedeuteration_woods_timecoursedeuteration_woods_timepointsdif_avedif_tpdif_tp_procduplicate_setsextreme_input_gapextreme_input_undeutgeneral_infogetCoords1heat_map_tcheat_map_tpheat_map_tp_maxuptakeheat_map_tp_maxuptake_procheat_map_tp_proclab_diflab_dif_proclab_vollegend_heat_maplegend_heat_map_tclegend_heat_map_timecourselegend_heat_map_tplegend_heat_map_tp_proclegend_nm_bottomlegend_raw_avelegend_raw_ave_proclegend_raw_ave_tclegend_sig_peptideslegend_states_PerD_bottomlegend_tc_bottomnb_exch_deutnm_statesoutput_FDoutput_FD_procoutput_prepoutput_tcoutput_tpoutput_UDoutput_UD_procpallette_legendpallette_llpeptide_pv_tppeptide_pv_tp_procpl_gen_ch2pl_gen_uptakeplot_heat_map_max_uptake_tpplot_heat_map_max_uptake_tp_procplot_heat_map_tcplot_heat_map_tpplot_heat_map_tp_procplot_peptide_sig_tpplot_peptide_sig_tp_procplots_av_tcourseplots_av_tpplots_av_tp_procplots_diff_tpplots_diff_tp_procplots_vol_tppparppar_bottom_legendppar_widerpparLMprep_timecourse_plot_aveprep_timecourse_plot_sdpv_timecoursepv_timepointpymol_script_average_residuepymol_script_significant_peptidepymol_script_significant_peptide_procpymol_script_significant_residuepymol_script_significant_residue_procpymol_strqpcr.cbind.naranges_functionranges_function_tcrbind_nareset_parrobot_2states_indexesrobot_indexesrobot_indexes_dfrobot_plot_Allsd_timecoursesd_timecourse_procsd_timepointselect_indicessignificant_peptide_uptakesummary_sd_CIuptake_plotsverbose_timecourse_outputverbose_timepoint_outputvol_tpwoods_CI_plot

Dependencies:clicpp11dplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangstringistringrtibbletidyrtidyselectutf8vctrswithrwrapr

HDXBoxeR

Maria K. Janowska, Katherine Reiter, Pearl Magala, Miklos Guttman, Rachel E. Klevit

Rendered fromHDXBoxeR.Rmdusingknitr::rmarkdownon Nov 17 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Returns full summary table.all_summary
Returns initially processed data.frame from the export from the HDXExaminerarg_df
Returns initially processed data.frame from the export from the HDXExaminerarg_UN_FD
Returns default arguments for the output_tp functions. Statesarguments_call1
Returns default arguments for the output_tp functions. Deut.Timearguments_call2
Returns default arguments for the output_tp functions. # replicatesarguments_call3
Preparatory function for average plot for timecoursesav_tc
Preparatory function for average plotav_tp
Returns average value for either uptake of procent data.ave_timepoint
Calculates average for time course data.average_timecourse
Summary of backexchange summarybackHX_calculations
Plots boxplots for all the averages in the setboxplot_tp
Global confidence interval treshold from experimental standard deviation for 2 samples.CI_2pts
Global confidence interval treshold from experimental standard deviation for 1 sampleCI_single
Critial interval calculation two sets of timecoursesCI_tc
Global confidence interval treshold from experimental standard deviationCI_tp
Returns color pallete from red to blue with number of colors for defined rangescolor_ranges_Blue_Red_heat_map
Returns Spectral pallette with colors matching defined rangescolor_ranges_Spectral
Returns coverage per residuecoverage_residue
Return woods plots for the timecoursedeuteration_woods_timecourse
Return woods plots for the timepointsdeuteration_woods_timepoints
Returns data frame with difference of averages between State1 and other states provided.dif_ave
Preparatory function for difference plotdif_tp
Preparatory function for difference plotdif_tp_proc
Duplicate set functionduplicate_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 packagegetCoords1
Plots heat maps for time courses.heat_map_tc
Preparatory function for heat mapheat_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 deuterationheat_map_tp_proc
Checks for NaN is data.frameis.nan.data.frame
Legend for difference in averages plot.lab_dif
Preparatory function for difference plot for procent deuterationlab_dif_proc
Preparatory function for volcano plot legendslab_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.framelegend_heat_map_tp
Legend for the heatmaps percent.Extracts names from data.framelegend_heat_map_tp_proc
Legend, bottom of the plotslegend_nm_bottom
Legend for average plot.legend_raw_ave
Preparatory function to draw legends for average procentlegend_raw_ave_proc
Legend for average deuteration plot for timecourse.legend_raw_ave_tc
Legend for the significant peptideslegend_sig_peptides
Legend, bottom of the plotslegend_states_PerD_bottom
Preparatory function returns legends for the timecourses.legend_tc_bottom
Number of exchangeable protonsnb_exch_deut
Lists names of states in data setsnm_states
Prepares output for HDX-MS Full deuteration dataoutput_FD
Prepares output for HDX-MS Full deuteration data for procent deuteration.output_FD_proc
Prepares output with HDX-MS data for publicationsoutput_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.framepallette_legend
Color scheme using heatmap. Legend extracts names from data framepallette_ll
Preparatory function for significant peptide plotspeptide_pv_tp
Preparatory function for showing peptides with significant differences between sets.peptide_pv_tp_proc
Prepares the plot window for the woods functionspl_gen_ch2
Prepares the plot window for the woods functionspl_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 frameplots_av_tp
Returns average procent deuteration plot for time pointsplots_av_tp_proc
Returns difference in average plot for timepoints in the data frameplots_diff_tp
Returns difference in average procent deuteration plot for timepoints in the data frameplots_diff_tp_proc
Returns volcano plots for timepoints in the data frameplots_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 marginspparLM
Prepares function for plotting averages in timecourseprep_timecourse_plot_ave
Prepares function for Critical interval for timecoursesprep_timecourse_plot_sd
pvalue calculation between two sets of the data at certain timepointpv_timecourse
Calculation of pvalue between first protein state and any other state from all_states filepv_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 peptidespymol_script_significant_peptide
Writes a text files with pymol scripts to list significant peptidespymol_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 scriptspymol_str
Hidden function from qpcR package, typical usage as qpcR:::cbind.naqpcr.cbind.na
Gives ranges for the averagesranges_function
Gives ranges for the averages for time course analysisranges_function_tc
bind non equal rowrbind_na
Reset plotting window parameters to defaultreset_par
Returns a robot plot for selected peptides for 2 protein states.robot_2states_indexes
Returns indexes for peptides with significant difference between two setsrobot_indexes
Returns dataframe with peptides which exhibit significant difference between two setsrobot_indexes_df
Returns a robot plot for comparisons of the timepoints samplesrobot_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 dataselect_indices
Function returns which peptides are significantly based of pv_cutoff and Critial intervalsignificant_peptide_uptake
Provides summary table with Critical interval and standard deviation within the set.summary_sd_CI
Uptake plotsuptake_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 plotvol_tp
Returns a woods plot for comparisons of the timepoints sampleswoods_CI_plot