create_uptake_dataset: Create uptake dataset for multiple states

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

Create uptake dataset for multiple states

Description

Calculates deuterium uptake values for selected biological states in multiple time points of measurements.

Usage

create_uptake_dataset(
  dat,
  protein = unique(dat[["Protein"]])[1],
  states = unique(dat[["State"]]),
  time_0 = min(dat[["Exposure"]]),
  time_100 = max(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat	data imported by the read_hdx function.
protein	chosen protein.
states	list of biological states for chosen protein.
time_0	minimal exchange control time point of measurement [min].
time_100	maximal exchange control time point of measurement [min].
deut_part	deuterium percentage in solution used in experiment, value from range [0, 1].

Details

Function create_uptake_dataset generates a dataset with deuterium uptake values in different forms. For each peptide in chosen protein in chosen states for time points of measurement between minimal and maximal control time points of measurement deuterium uptake, fractional deuterium uptake with respect to controls or theoretical tabular values are calculated, with combined and propagated uncertainty. Each peptide has an ID, based on its start position. This function is a wrapper for create_state_uptake_dataset but for multiple states. The output of this function can be presented in a form of comparison plot.

Value

a data.frame object.

See Also

read_hdx calculate_state_uptake create_state_uptake_dataset

Examples

uptake_dat <- create_uptake_dataset(alpha_dat, states = c("Alpha_KSCN", "ALPHA_Gamma"))
head(uptake_dat)

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