Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

Documentation for package ‘HDXBoxeR’ version 0.0.1

Help Pages

-- 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 --

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