calculate_state_deuteration {HaDeX}

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
)

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.

Value

a data.frame object

See Also

read_hdx calculate_confidence_limit_values add_stat_dependency

Examples

# 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)