Calculates deuteration uptake based on supplied parameters.

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]

Value

a data.frame object

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.

See also

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)
#> # A tibble: 41 x 14 #> Protein Sequence Start End State frac_exch_state err_frac_exch_s… #> <chr> <chr> <int> <int> <chr> <dbl> <dbl> #> 1 db_CD1… INITSSA… 1 15 CD160 87.6 0.395 #> 2 db_CD1… LICTVW 16 21 CD160 41.7 0.346 #> 3 db_CD1… LICTVWH… 16 29 CD160 72.1 0.711 #> 4 db_CD1… ICTVWHK… 17 29 CD160 75.6 0.520 #> 5 db_CD1… FVVFL 30 34 CD160 40.1 1.23 #> 6 db_CD1… LCKDRSG… 34 48 CD160 97.6 0.368 #> 7 db_CD1… LCKDRSG… 34 49 CD160 97.2 0.331 #> 8 db_CD1… LCKDRSG… 34 51 CD160 95.3 0.240 #> 9 db_CD1… LCKDRSG… 34 69 CD160 93.6 0.222 #> 10 db_CD1… CKDRSGD… 35 48 CD160 97.2 0.462 #> # … with 31 more rows, and 7 more variables: abs_frac_exch_state <dbl>, #> # err_abs_frac_exch_state <dbl>, avg_theo_in_time <dbl>, #> # err_avg_theo_in_time <dbl>, abs_avg_theo_in_time <dbl>, #> # err_abs_avg_theo_in_time <dbl>, Med_Sequence <dbl>