test_houde: Houde's test for deuteration curves

In hadexversum/powerHDX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis

Houde's test for deuteration curves

Description

This function performs Damian Houde's confidence intervals test for differences in deuteration levels. Its input and output are compatible with the function calculate_hdx_power.

Usage

test_houde(data, significance_level = 0.05)

Arguments

data	data.table with deuteration curves
significance_level	significance level for tests

Value

This function returns a data table compatible with the function calculate_hdx_power.

References

Houde, Damian, Steven A Berkowitz, and John R Engen (2011). “The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparabilitystudies”. In:Journal of pharmaceutical sciences100.6, pp. 2071–2086.

See Also

Other tests:

- test_hdx_analyzer

- test_memhdx_model

-test_semiparametric

Or calculate_hdx_power for estimation of power of tests for differences in deuteration levels.

Examples

theo_spectra_pf_100 <- simulate_theoretical_spectra(sequence = "LVRKDLQN",
                                                    charge = c(3, 5),
                                                    protection_factor = 100,
                                                    times = c(0.167, 5),
                                                    pH = 7.5,
                                                    temperature = 15,
                                                    n_molecules = 500,
                                                    time_step_const = 1,
                                                    use_markov = TRUE)
theo_spectra_pf_200 <- simulate_theoretical_spectra(sequence = "LVRKDLQN",
                                                    charge = c(3, 5),
                                                    protection_factor = 200,
                                                    times = c(0.167, 5),
                                                    pH = 7.5,
                                                    temperature = 15,
                                                    n_molecules = 500,
                                                    time_step_const = 1,
                                                    use_markov = TRUE)

theo_spectra_two_states <- rbind(theo_spectra_pf_100, theo_spectra_pf_200)

deut_curves_p_states <- get_noisy_deuteration_curves(theo_spectra_two_states,
                                                     n_replicates = 4,
                                                     n_experiments = 1,
                                                     reference = 100)[[1]][[1]]
test_houde(deut_curves_p_states)

hadexversum/powerHDX documentation built on Aug. 31, 2022, 7:47 p.m.