Package index
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calculate_recovered_uc_rmse()
- Calculate rmse of recovered deuterium uptake
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calculate_replicate_state_uptake()
- Calculcate uptake
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calculate_uc_from_hires_peptide()
- Recovers deuterium uptake from hi-res parameters
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compare_aggregation_methods()
- Compare aggregation methods
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create_fit_dataset()
- Create fits for the whole peptide pool
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create_replicate_state_uptake_dataset()
- Creates deuterium uptake replicate dataset
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create_two_state_dataset()
- Creates dataset with merged hires parameters for two states.
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create_uc_distance_dataset()
- Creates dataset with uc distances
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create_uc_from_hires_dataset()
- Creates recovered deuterium uptake dataset
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get_example_control()
- Example control
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get_example_fit_k_params()
- Example k parameters
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get_example_fit_k_params_2()
- Example k parameters
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get_fit_results()
- Uptake curve fitting function
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get_params_summary_image()
- Plot summary image
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get_peptide_list()
- Provides a peptide list
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get_peptide_list_v2()
- Provides a peptide list
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get_residue_positions()
- Get a data table with positions and residues
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get_uc_distance()
- Calculates the uc distance for uptake curve
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hradexify()
- HRaDeX customized ggplot theme
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omit_amino()
- Omit first amino of peptides
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plot_3d_structure_blank()
- Plots blank 3D structure
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plot_3d_structure_hires()
- Presents classification results on 3D structure
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plot_class_heatmap()
- Plots heatmap with classification parameters
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plot_color_distance()
- Plots assigned color distance
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plot_cov_class()
- Plots coverage with classification results
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plot_double_uc()
- Plots two uc plots side by side
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plot_estimated_k()
- Plots estimated k
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plot_fitted_uc()
- Plots uptake curve with fit components
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plot_hires()
- Plots high resolution classification plot
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plot_interactive()
- Wrapper for interactivity
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plot_k_distance()
- Plots estimated k distance
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plot_lm()
- Plots uc with linear fit
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plot_n()
- Plots n values
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plot_params_map()
- Plots map of params
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plot_recovered_uc_coverage()
- Plots recovered DU rmse
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plot_rss_hist()
- Histogram of fit rss values
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plot_singular_uc()
- Plots singular uptake curve
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plot_start_params()
- Plots initial fit parameters
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plot_two_states()
- Plots the classification results for two states
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plot_uc()
- Plots uc and fit parameters for peptide in two states.
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plot_uc_distance()
- Plots the uc difference type 2
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plot_uc_real_dist()
- Plots the uc difference type 1
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prepare_diff_data()
- Prepares differential data
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prepare_kin_dat()
- Creates uptake data from mass measurements
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recreate_uc()
- Plots recovered DU of a peptide