Package index • HRaDeX

All functions

calculate_recovered_uc_rmse(): Calculate rmse of recovered deuterium uptake

calculate_replicate_state_uptake(): Calculcate uptake

calculate_uc_from_hires_peptide(): Recovers deuterium uptake from hi-res parameters

compare_aggregation_methods(): Compare aggregation methods

create_fit_dataset(): Create fits for the whole peptide pool

create_replicate_state_uptake_dataset(): Creates deuterium uptake replicate dataset

create_two_state_dataset(): Creates dataset with merged hires parameters for two states.

create_uc_distance_dataset(): Creates dataset with uc distances

create_uc_from_hires_dataset(): Creates recovered deuterium uptake dataset

export_chimera_commands(): Export coloring commands for ChimeraX

get_dominant_class(): Get get dominant class and color from hires data

get_example_control(): Example control

get_example_fit_k_params(): Example k parameters

get_example_fit_k_params_2(): Example k parameters

get_fit_results(): Uptake curve fitting function

get_params_summary_image(): Plot summary image

get_peptide_list(): Provides a peptide list

get_peptide_list_v2(): Provides a peptide list

get_residue_positions(): Get a data table with positions and residues

get_uc_distance(): Calculates the uc distance for uptake curve

hradexify(): HRaDeX customized ggplot theme

omit_amino(): Omit first amino of peptides

plot_3d_structure_blank(): Plots blank 3D structure

plot_3d_structure_dominant(): Plot dominant class on 3D structure

plot_3d_structure_hires(): Presents classification results on 3D structure

plot_class_heatmap(): Plots heatmap with classification parameters

plot_color_distance(): Plots assigned color distance

plot_cov_class(): Plots coverage with classification results

plot_double_uc(): Plots two uc plots side by side

plot_estimated_k(): Plots estimated k

plot_fitted_uc(): Plots uptake curve with fit components

plot_hires(): Plots high resolution classification plot

plot_interactive(): Wrapper for interactivity

plot_k_distance(): Plots estimated k distance

plot_lm(): Plots uc with linear fit

plot_n(): Plots n values

plot_params_map(): Plots map of params

plot_recovered_uc_coverage(): Plots recovered DU rmse

plot_rss_hist(): Histogram of fit rss values

plot_singular_uc(): Plots singular uptake curve

plot_start_params(): Plots initial fit parameters

plot_two_states(): Plots the classification results for two states

plot_uc(): Plots uc and fit parameters for peptide in two states.

plot_uc_distance(): Plots the uc difference type 2

plot_uc_real_dist(): Plots the uc difference type 1

prepare_diff_data(): Prepares differential data

prepare_kin_dat(): Creates uptake data from mass measurements

recreate_uc(): Plots recovered DU of a peptide