calculate_state_deuteration: Calculate deuteration

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

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)

michbur/HaDeX documentation built on March 29, 2022, 5:46 p.m.