calculate_state_deuteration: Calculate deuteration

Description

Calculates deuteration uptake based on supplied parameters.

Usage

calculate_state_deuteration(
  dat,
  protein,
  state,
  time_in,
  time_chosen,
  time_out,
  deut_part = 1
)

Value

a data.frame object

Arguments

dat: data as imported by the read_hdx function
protein: protein included in calculations
state: state included in calculations
time_in: experimental `time_in`
time_chosen: chosen time point
time_out: experimental `time_out`
deut_part: percentage of deuterium the protein was exposed to, value in range [0, 1]

Details

The function calculate_state_deuteration calculates deuteration for peptides in given protein in given state based on supplied parameters: `time_in`, `time_out` and `time_chosen`. All four variants (combinations of theoretical & relative) 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.

Examples

Run this code

# load example data
dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv"))

# calculate deuteration for state "CD160"
calculate_state_deuteration(dat, protein = "db_CD160", state = "CD160",
                            time_in = 0, time_chosen = 5.000, time_out = 1440.000)