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Power calculations for Hydrogen/Deuterium Exchange experiments

This R package implements methods for

  • simulation of isotope distribution of deuterated peptides (theoretical spectra) based on the code provided by Zhong-Yuan Kan,

  • creating deuteration curves based on theoretical spectra with multiple technical replicates and a given error structure,

  • testing differential deuterium uptake,

  • power calculations for Hydrogen/Deuterium Exchange experiments.

Development version can be downloaded from Github:

if (!require(devtools)) {
  install.packages('devtools')
}
devtools::install_github("hadexversum/powerHaDeX")

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Version

Install

install.packages('powerHaDeX')

Monthly Downloads

39

Version

1.0

License

GPL (>= 3)

Maintainer

Krystyna Grzesiak

Last Published

January 24th, 2022

Functions in powerHaDeX (1.0)

get_deuteration_curves_from_spectra

Calculate deuteration curves
get_deuteration_single_timepoint

Calculates deuteration for given timepoint
get_iso_probs_deut

Calculate isotopic probabilities (intensity) and mass-to-charge ratio (m/z).
get_exchange_rates

Hydrogen-deuterium or back-exchange exchange rates
plot_spectra

Draw mass spectra
get_HD_matrices

Get a matrix of simulated exchanged hydrogens for each experiment time point
get_exchange_constants

Exchange constant for Hydrogen-Deuterium Exchange.
get_exchange_probabilities

Get probability of an exchange (HD and DH)
powerHDX-package

A short title line describing what the package does
add_noise_to_intensities

Adds noise to a single time point in intensity domain
test_hdx_analyzer

HDX-Analyzer model
get_approx_isotopic_distribution

Approximates isotopic distribution
get_deuteration_curve_single_spectrum

Get a deuteration curve from a single spectrum
fix_columns_names_types

Standardize column names and types
get_HD_matrices_using_markov

Get a matrix of simulated exchanged hydrogens for each experiment time point using markov chains
create_experimental_file

Create experimental file
get_observed_iso_dist

Get observed distribution of ions
powerHaDeX

powerHaDeX
get_noisy_deuteration_curves

Replicated deuterium uptake curves
prepare_input_peptides

convert_hadex_data

Convert HaDeX to powerHaDeX data type.
simulate_theoretical_spectra

Simulate theoretical spectra of a deuterated peptide over time
test_hadex_data

Apply tests for HaDeX data
test_houde

Houde's test for deuteration curves
truncated_lines

Get truncated lines
get_paired_spectra

Get list of data.tables of spectra for pairs of protection factors
get_F_const

F constants
get_poly_const

Constant related to...
get_relative_mass

Get relative mass
make_noisy_spectra

Creates spectra with technical replicates and noise
get_undeuterated_mass

Mass of an undeuterated peptide
get_pkc

Calculating pKc values
make_experimental_design

Create a list of spectra with replicates from a list of spectra
test_memhdx_model

MEMHDX model
get_spectra_list

Get a list of spectra
test_semiparametric

Semiparametric test for differences in deuteration levels
calculate_hdx_power

Calculate power of statistical tests for HDX experiments
add_noise_to_curves

Adds noise to deuteration curves
calculate_peptide_mass

Peptide mass
add_column

Complete data frame with columns
add_noise_to_single_curve

Adds noise to a single deuteration curve
add_noise_to_one_timepoint

Adds noise to a single time point in mass domain
add_noise_to_one_spectrum

Add noise to a single spectrum
add_noise_to_spectra

Creates spectra with technical replicates and noise
add_noise

Adds noise to mass domain