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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
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_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