test_memhdx_model: MEMHDX model

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

MEMHDX model

Description

This function performs the test based on a linear mixed effects model used in MEMHDX tools. Its input and output are compatible with the function calculate_hdx_power.

Usage

test_memhdx_model(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

Hourdel, Véronique et al. (July 2016). “MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS data sets”. In:Bioinformatics32.22, pp. 3413–3419.issn: 1367-4803.

See Also

Other tests:

- test_houde

- test_hdx_analyzer

-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_memhdx_model(deut_curves_p_states)

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