calculate_state_uptake: Calculate deuterium uptake

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

Calculate deuterium uptake

Description

Calculates deuteration uptake based on supplied parameters.

Usage

calculate_state_uptake(
  dat,
  protein = unique(dat[["Protein"]])[1],
  state = unique(dat[["State"]])[1],
  time_0 = min(dat[dat[["Exposure"]] > 0, ][["Exposure"]]),
  time_t = unique(dat[["Exposure"]])[3],
  time_100 = max(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat	data as imported by the read_hdx function
protein	chosen protein
state	state included in calculations
time_0	minimal exchange control
time_t	chosen time point
time_100	maximal exchange control
deut_part	percentage of deuterium the protein was exposed to, value in range [0, 1]

Details

The function calculate_state_uptake calculates deuterium uptake (in different forms) for all of the peptides in given protein in given state based on supplied parameters: 'time_0', 'time_100' and 'time_t'. All four variants (fractional) are supplied (mean values and uncertainty). Manual correction of percentage of deuterium the protein was exposed to during the exchange in theoretical calculations is provided.

Methods of calculation and uncertainty are profoundly discussed in the vignette.

Value

a data.frame object

See Also

read_hdx create_uptake_dataset calculate_confidence_limit_values add_stat_dependency

Examples

head(calculate_state_uptake(alpha_dat))
                            

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