calculate_state_deuteration.RdCalculates deuteration uptake based on supplied parameters.
calculate_state_deuteration( dat, protein, state, time_in, time_chosen, time_out, deut_part = 1 )
| dat | data as imported by the |
|---|---|
| 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] |
a data.frame object
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.
# 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 0.592 #> 2 db_CD1~ LICTVW 16 21 CD160 41.7 0.581 #> 3 db_CD1~ LICTVWH~ 16 29 CD160 72.1 1.07 #> 4 db_CD1~ ICTVWHK~ 17 29 CD160 75.6 0.780 #> 5 db_CD1~ FVVFL 30 34 CD160 40.1 1.85 #> 6 db_CD1~ LCKDRSG~ 34 48 CD160 97.6 0.552 #> 7 db_CD1~ LCKDRSG~ 34 49 CD160 97.2 0.497 #> 8 db_CD1~ LCKDRSG~ 34 51 CD160 95.3 0.359 #> 9 db_CD1~ LCKDRSG~ 34 69 CD160 93.6 0.336 #> 10 db_CD1~ CKDRSGD~ 35 48 CD160 97.2 0.693 #> # ... 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>