# Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

## Documentation for package ‘HDXBoxeR’ version 0.0.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

A B C D E G H I L N O P Q R S U V W

## -- A --

all_summary | Returns full summary table.
arguments_call1 | Returns default arguments for the output_tp functions. States
arguments_call2 | Returns default arguments for the output_tp functions. Deut.Time
arguments_call3 | Returns default arguments for the output_tp functions. # replicates
arg_df | Returns initially processed data.frame from the export from the HDXExaminer
arg_UN_FD | Returns initially processed data.frame from the export from the HDXExaminer
average_timecourse | Calculates average for time course data.
ave_timepoint | Returns average value for either uptake of procent data.
av_tc | Preparatory function for average plot for timecourses
av_tp | Preparatory function for average plot

## -- B --

backHX_calculations | Summary of backexchange summary
boxplot_tp | Plots boxplots for all the averages in the set

## -- C --

CI_2pts | Global confidence interval treshold from experimental standard deviation for 2 samples.
CI_single | Global confidence interval treshold from experimental standard deviation for 1 sample
CI_tc | Critial interval calculation two sets of timecourses
CI_tp | Global confidence interval treshold from experimental standard deviation
color_ranges_Blue_Red_heat_map | Returns color pallete from red to blue with number of colors for defined ranges
color_ranges_Spectral | Returns Spectral pallette with colors matching defined ranges
coverage_residue | Returns coverage per residue

## -- D --

deuteration_woods_timecourse | Return woods plots for the timecourse
deuteration_woods_timepoints | Return woods plots for the timepoints
dif_ave | Returns data frame with difference of averages between State1 and other states provided.
dif_tp | Preparatory function for difference plot
dif_tp_proc | Preparatory function for difference plot
duplicate_sets | Duplicate set function

## -- E --

extreme_input_gap | Makes input for Extreme for bimodal analysis.
extreme_input_undeut | Makes input for Extreme for bimodal analysis.

## -- G --

general_info | Provides summary table for all data.sets.
getCoords1 | function from plotfunctions package

## -- H --

heat_map_tc | Plots heat maps for time courses.
heat_map_tp | Preparatory function for heat map
heat_map_tp_maxuptake | Preparatory function for heat map of maximum uptake per residue.
heat_map_tp_maxuptake_proc | Preparatory function for heat map of maximum procent deuteration per residue.
heat_map_tp_proc | Preparatory function for heat map for procent deuteration

## -- I --

is.nan.data.frame | Checks for NaN is data.frame

## -- L --

lab_dif | Legend for difference in averages plot.
lab_dif_proc | Preparatory function for difference plot for procent deuteration
lab_vol | Preparatory function for volcano plot legends
legend_heat_map | Legend for the heatmaps prep function.
legend_heat_map_tc | Legend for the heatmaps for timecourses.
legend_heat_map_timecourse | Legend for the heatmaps prep function for timecourses.
legend_heat_map_tp | Legend for the heatmaps.Extracts names from data.frame
legend_heat_map_tp_proc | Legend for the heatmaps percent.Extracts names from data.frame
legend_nm_bottom | Legend, bottom of the plots
legend_raw_ave | Legend for average plot.
legend_raw_ave_proc | Preparatory function to draw legends for average procent
legend_raw_ave_tc | Legend for average deuteration plot for timecourse.
legend_sig_peptides | Legend for the significant peptides
legend_states_PerD_bottom | Legend, bottom of the plots
legend_tc_bottom | Preparatory function returns legends for the timecourses.

## -- N --

nb_exch_deut | Number of exchangeable protons
nm_states | Lists names of states in data sets

## -- O --

output_FD | Prepares output for HDX-MS Full deuteration data
output_FD_proc | Prepares output for HDX-MS Full deuteration data for procent deuteration.
output_prep | Prepares output with HDX-MS data for publications
output_tc | Prepares output for HDX-MS for the deuteration uptake or percent deuteration for the time courses.
output_tp | Prepares output for HDX-MS for the deuteration uptake or percent deuteration for the time points.
output_UD | Prepares output for HDX-MS Undeuterated sample data.
output_UD_proc | Prepares output for HDX-MS Undeuterated data for procent deuteration.

## -- P --

pallette_legend | Color scheme using heatmap. Legend Extracts names from data.frame
pallette_ll | Color scheme using heatmap. Legend extracts names from data frame
peptide_pv_tp | Preparatory function for significant peptide plots
peptide_pv_tp_proc | Preparatory function for showing peptides with significant differences between sets.
plots_av_tcourse | Generates average deuteration plot for the time-course.
plots_av_tp | Returns average deuteration plot for timepoints in the data frame
plots_av_tp_proc | Returns average procent deuteration plot for time points
plots_diff_tp | Returns difference in average plot for timepoints in the data frame
plots_diff_tp_proc | Returns difference in average procent deuteration plot for timepoints in the data frame
plots_vol_tp | Returns volcano plots for timepoints in the data frame
plot_heat_map_max_uptake_tp | Plots heat maps for maximum uptake per residue.
plot_heat_map_max_uptake_tp_proc | Plots heat maps for maximum procent deuteration per residue.
plot_heat_map_tc | Plots heat maps for time courses.
plot_heat_map_tp | Plots heat maps for significant peptides.
plot_heat_map_tp_proc | Plots heat maps for significant peptides.
plot_peptide_sig_tp | Significant peptide plots.
plot_peptide_sig_tp_proc | Draws peptides with significant difefrences between sets.
pl_gen_ch2 | Prepares the plot window for the woods functions
pl_gen_uptake | Prepares the plot window for the woods functions
ppar | Preparation of figure window.
pparLM | Preparation of figure window. small margins
ppar_bottom_legend | Preparation of figure window with area for figure at the bottom.
ppar_wider | Preparation of figure window with more area on west side of plot.
prep_timecourse_plot_ave | Prepares function for plotting averages in timecourse
prep_timecourse_plot_sd | Prepares function for Critical interval for timecourses
pv_timecourse | pvalue calculation between two sets of the data at certain timepoint
pv_timepoint | Calculation of pvalue between first protein state and any other state from all_states file
pymol_script_average_residue | Writes a text files with pymol scripts to list significant residues.
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 peptides
pymol_script_significant_residue | Writes a text files with pymol scripts to list significant residues.
pymol_script_significant_residue_proc | Writes a text files with pymol scripts to list significant residues.
pymol_str | Preparatory function writing pymol scripts

## -- Q --

qpcr.cbind.na | Hidden function from qpcR package, typical usage as qpcR:::cbind.na

## -- R --

ranges_function | Gives ranges for the averages
ranges_function_tc | Gives ranges for the averages for time course analysis
rbind_na | bind non equal row
reset_par | Reset plotting window parameters to default
robot_2states_indexes | Returns a robot plot for selected peptides for 2 protein states.
robot_indexes | Returns indexes for peptides with significant difference between two sets
robot_indexes_df | Returns dataframe with peptides which exhibit significant difference between two sets
robot_plot_All | Returns a robot plot for comparisons of the timepoints samples

## -- S --

sd_timecourse | Returns standard deviation for uptake data for timecourses.
sd_timecourse_proc | Returns standard deviation for percent deuteration data for timecourses.
sd_timepoint | Returns standard deviation for dataframe.
select_indices | Allows for selecting some peptide from input data
significant_peptide_uptake | Function returns which peptides are significantly based of pv_cutoff and Critial interval
summary_sd_CI | Provides summary table with Critical interval and standard deviation within the set.

## -- U --

uptake_plots | Uptake plots

## -- V --

verbose_timecourse_output | Returns csv with averages from analysis for procent deuteration file, standard deviation for time courses.
verbose_timepoint_output | Returns csv with averages from analysis for uptake file, standard deviation, p-values.
vol_tp | Preparatory function for volcano plot

## -- W --

woods_CI_plot | Returns a woods plot for comparisons of the timepoints samples