powerHaDeX (version 1.0)

test_hdx_analyzer: HDX-Analyzer model

Description

This function performs the test based on the simplest linear models for deuteration curves containing time, state of the protein and the interaction term. Its input and output are compatible with the function calculate_hdx_power.

Usage

test_hdx_analyzer(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

Liu, Sanmin et al. (2011). <U+201C>HDX-analyzer: a novel package for statistical analysis of protein structure dynamics<U+201D>. In:BMC bioinformatics12.1, pp. 1<U+2013>10.

See Also

Other tests:

- test_houde

- test_memhdx_model

-test_semiparametric

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

Examples

# NOT RUN {
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_hdx_analyzer(deut_curves_p_states)

# }