Man pages for hadexversum/powerHaDeX
Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis
| add_column | Complete data frame with columns |
| add_noise | Adds noise to mass domain |
| add_noise_to_curves | Adds noise to deuteration curves |
| add_noise_to_intensities | Adds noise to a single time point in intensity domain |
| add_noise_to_one_spectrum | Add noise to a single spectrum |
| add_noise_to_one_timepoint | Adds noise to a single time point in mass domain |
| add_noise_to_single_curve | Adds noise to a single deuteration curve |
| add_noise_to_spectra | Creates spectra with technical replicates and noise |
| calculate_hdx_power | Calculate power of statistical tests for HDX experiments |
| calculate_peptide_mass | Peptide mass |
| convert_hadex_data | Convert HaDeX to powerHaDeX data type. |
| create_experimental_file | Create experimental file |
| fix_columns_names_types | Standardize column names and types |
| get_approx_isotopic_distribution | Approximates isotopic distribution |
| get_deuteration_curves_from_spectra | Calculate deuteration curves |
| get_deuteration_curve_single_spectrum | Get a deuteration curve from a single spectrum |
| get_deuteration_single_timepoint | Calculates deuteration for given timepoint |
| get_exchange_constants | Exchange constant for Hydrogen-Deuterium Exchange. |
| get_exchange_probabilities | Get probability of an exchange (HD and DH) |
| get_exchange_rates | Hydrogen-deuterium or back-exchange exchange rates |
| get_F_const | F constants |
| get_HD_matrices | Get a matrix of simulated exchanged hydrogens for each... |
| get_HD_matrices_using_markov | Get a matrix of simulated exchanged hydrogens for each... |
| get_iso_probs_deut | Calculate isotopic probabilities (intensity) and... |
| get_noisy_deuteration_curves | Replicated deuterium uptake curves |
| get_observed_iso_dist | Get observed distribution of ions |
| get_paired_spectra | Get list of data.tables of spectra for pairs of protection... |
| get_pkc | Calculating pKc values |
| get_poly_const | Constant related to... |
| get_relative_mass | Get relative mass |
| get_spectra_list | Get a list of spectra |
| get_undeuterated_mass | Mass of an undeuterated peptide |
| make_experimental_design | Create a list of spectra with replicates from a list of... |
| make_noisy_spectra | Creates spectra with technical replicates and noise |
| plot_spectra | Draw mass spectra |
| powerHaDeX | powerHaDeX |
| powerHDX-package | A short title line describing what the package does |
| prepare_input_peptides | Prepare input for 'create_experimental_file' |
| simulate_theoretical_spectra | Simulate theoretical spectra of a deuterated peptide over... |
| test_hadex_data | Apply tests for HaDeX data |
| test_hdx_analyzer | HDX-Analyzer model |
| test_houde | Houde's test for deuteration curves |
| test_memhdx_model | MEMHDX model |
| test_semiparametric | Semiparametric test for differences in deuteration levels |
| truncated_lines | Get truncated lines |
