test_semiparametric: Semiparametric test for differences in deuteration levels

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

Semiparametric test for differences in deuteration levels

Description

This function performs the semiparametric test for differences in deuteration levels. Its input and output are compatible with the function calculate_hdx_power.

Usage

test_semiparametric(data, significance_level = 0.05)

Arguments

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

Details

This function uses truncated_lines. The knots considered in the testing procedure are chosen using ridge regression.

Value

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

See Also

Other tests:

- test_houde

- test_hdx_analyzer

-test_memhdx_model

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, 10, 30),
                                                    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, 10, 30),
                                                    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_semiparametric(deut_curves_p_states)

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