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
all_summary             Returns full summary table.
arg_UN_FD               Returns initially processed data.frame from the
                        export from the HDXExaminer
arg_df                  Returns initially processed data.frame from the
                        export from the HDXExaminer
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
av_tc                   Preparatory function for average plot for
                        timecourses
av_tp                   Preparatory function for average plot
ave_timepoint           Returns average value for either uptake of
                        procent data.
average_timecourse      Calculates average for time course data.
backHX_calculations     Summary of backexchange summary
boxplot_tp              Plots boxplots for all the averages in the set
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
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
extreme_input_gap       Makes input for Extreme for bimodal analysis.
extreme_input_undeut    Makes input for Extreme for bimodal analysis.
general_info            Provides summary table for all data.sets.
getCoords1              function from plotfunctions package
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
is.nan.data.frame       Checks for NaN is data.frame
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.
nb_exch_deut            Number of exchangeable protons
nm_states               Lists names of states in data sets
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_UD               Prepares output for HDX-MS Undeuterated sample
                        data.
output_UD_proc          Prepares output for HDX-MS Undeuterated 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.
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.
pl_gen_ch2              Prepares the plot window for the woods
                        functions
pl_gen_uptake           Prepares the plot window for the woods
                        functions
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.
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
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
qpcr.cbind.na           Hidden function from qpcR package, typical
                        usage as qpcR:::cbind.na
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
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.
uptake_plots            Uptake plots
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
woods_CI_plot           Returns a woods plot for comparisons of the
                        timepoints samples
