Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

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Documentation for package ‘HaDeX2’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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