calculate_p_value: Create p-value dataset

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Create p-value dataset

Description

Create p-value dataset

Usage

calculate_p_value(
  dat,
  protein = unique(dat[["Protein"]])[1],
  state_1 = unique(dat[["State"]])[1],
  state_2 = unique(dat[["State"]])[2],
  p_adjustment_method = "none",
  confidence_level = 0.98
)

Arguments

dat	data imported by the read_hdx function.
protein	chosen protein.
state_1	biological state for chosen protein. From this state values the second state values are subtracted to get the deuterium uptake difference.
state_2	biological state for chosen protein. This state values are subtracted from the first state values to get the deuterium uptake difference.
p_adjustment_method	method of adjustment P-values for multiple comparisons. Possible methods: "BH" (Benjamini & Hochberg correction), "bonferroni" (Bonferroni correction) and "none" (default).
confidence_level	confidence level for the t-test.

Details

This function calculates P-value based on the supplied data. Unpaired t-Student test (with supplied parameters) is used to establish if the null hypothesis (there is no difference between measured mass values between two selected biological states) can be rejected, based on the experimental mass values from replicates of the experiment - for peptide in given time point of measurement. For the peptides that have only one replicate of the measurement (in any state) the P-value cannot be calculated and is assigned with NA value.

Value

a data.frame object.

See Also

read_hdx calculate_exp_masses_per_replicate plot_volcano create_diff_uptake_dataset create_p_diff_uptake_dataset

Examples

p_dat <- calculate_p_value(alpha_dat)
head(p_dat)

HaDeX2 documentation built on Feb. 9, 2026, 5:07 p.m.