Package index • HaDeX

All functions

HaDeX-package HaDeX: HaDeX

HaDeX_GUI(): HaDeX Graphical User Interface

HaDeXify(): HaDeX customized ggplot theme

add_stat_dependency(): Calculates confidence limits

alpha_dat: Elongation factor eEF1B subunit alpha

calculate_MHP(): Calculate MHP of the peptide

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_p_value(): Create p-value dataset

calculate_peptide_kinetics(): Calculate kinetics 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

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_p_diff_uptake_data(): Differential deuterium uptake data

show_peptide_charge_measurement(): Show peptide charge measurement

show_peptide_mass_measurement(): Show peptide mass measurement

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