# Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

## Documentation for package ‘HaDeX2’ version 1.0.0

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

## Help Pages

HaDeX2-package | HaDeX2
add_stat_dependency | Calculates confidence limits
alpha_dat | Elongation factor eEF1B subunit alpha
calculate_aggregated_diff_uptake | Calculates aggregated deuterium uptake difference for one time point
calculate_aggregated_test_results | Aggregate test result
calculate_aggregated_uptake | Calculates aggregated deuterium uptake for one time point
calculate_auc | Calculate Area Under the Curve
calculate_back_exchange | Back exchange estimation
calculate_confidence_limit_values | Calculate the value of confidence limit
calculate_diff_uptake | Calculate differential uptake
calculate_exp_masses | Calculate measured mass, aggregated from the replicates of the experiment
calculate_exp_masses_per_replicate | Calculate measured mass for each replicate of the experiment
calculate_kinetics | Calculate kinetics data
calculate_MHP | Calculate MHP of the peptide
calculate_peptide_kinetics | Calculate kinetics dataset
calculate_p_value | Create p-value dataset
calculate_state_uptake | Calculate deuterium uptake
create_aggregated_diff_uptake_dataset | Calculates aggregated uptake difference for peptide pool
create_aggregated_uptake_dataset | Calculates the aggregated uptake for peptide pool
create_control_dataset | Create dataset with control
create_diff_uptake_dataset | Generate differential dataset
create_kinetic_dataset | Create kinetics dataset for a list of peptides and their states
create_overlap_distribution_dataset | Show overlap distribution data
create_p_diff_uptake_dataset | Create differential uptake dataset with p-value
create_p_diff_uptake_dataset_with_confidence | Create differential dataset with statistical validity
create_quality_control_dataset | Experiment quality control
create_replicate_dataset | Create replicates data
create_state_comparison_dataset | Creates comparison uptake dataset
create_state_uptake_dataset | Create uptake dataset for chosen state
create_uptake_dataset | Create uptake dataset for multiple states
get_n_replicates | Get number of replicates
get_peptide_sequence | Get peptide sequence based on the position
get_protein_coverage | Get protein coverage
get_protein_redundancy | Get protein redundancy
get_replicate_list_sd | Get replicates sd
get_residue_positions | Get residue positions
get_structure_color | Get color palette for 3D structure
HaDeX2 | HaDeX2
HaDeXify | HaDeX customized ggplot theme
HaDeX_GUI | HaDeX Graphical User Interface
install_GUI | Installs GUI package from GitHub
is_GUI_installed | Checks if GUI package is installed
plot_aggregated_differential_uptake | Plots aggregated uptake difference
plot_aggregated_uptake | Plots aggregated uptake
plot_aggregated_uptake_structure | Plot aggregated uptake on the 3D structure
plot_amino_distribution | generate_amino_distribution
plot_butterfly | Butterfly deuterium uptake plot
plot_chiclet | Chiclet deuterium uptake plot
plot_coverage | Peptide coverage
plot_coverage_heatmap | Coverage heatmap
plot_differential | Differential plot
plot_differential_butterfly | Butterfly differential deuterium uptake plot
plot_differential_chiclet | Chiclet differential deuterium uptake plot
plot_differential_uptake_curve | Plot differential uptake curve
plot_manhattan | Manhattan plot
plot_overlap | Plot overlap data
plot_overlap_distribution | Plot overlap distribution
plot_peptide_charge_measurement | Plot peptide charge measurement
plot_peptide_mass_measurement | Plot peptide mass measurement
plot_position_frequency | Position frequency
plot_quality_control | Plot quality control data
plot_replicate_histogram | Plot replicates histogram
plot_replicate_mass_uptake | Replicate mass uptake curve
plot_state_comparison | State deuterium uptake comparison
plot_uncertainty | Uncertainty of the peptide measurements
plot_uptake_curve | Deuterium uptake curve
plot_volcano | Volcano plot
prepare_hdxviewer_export | Prepares data export for HDX-Viewer
read_hdx | Read HDX-MS data file
reconstruct_sequence | Reconstruct protein sequence
show_aggregated_uptake_data | Show aggregated values in friendly form
show_coverage_heatmap_data | Coverage heatmap data
show_diff_uptake_data | Differential deuterium uptake data
show_diff_uptake_data_confidence | Differential uptake data with confidence
show_overlap_data | Show data on peptide overlap
show_peptide_charge_measurement | Show peptide charge measurement
show_peptide_mass_measurement | Show peptide mass measurement
show_p_diff_uptake_data | Differential deuterium uptake data
show_quality_control_data | Show quality control data
show_replicate_histogram_data | Show replicate data
show_summary_data | Summary data
show_uc_data | Deuterium uptake curve data
show_uptake_data | Deuterium uptake data
update_hdexaminer_file | Update HDeXaminer datafile