Calculate deuterium uptake

Calculates deuteration uptake based on supplied parameters.

Usage

calculate_state_uptake(
  dat,
  protein = unique(dat[["Protein"]])[1],
  state = unique(dat[["State"]])[1],
  time_0 = min(dat[dat[["Exposure"]] > 0, ][["Exposure"]]),
  time_t = unique(dat[["Exposure"]])[3],
  time_100 = max(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat

data as imported by the read_hdx function

protein

chosen protein

state

state included in calculations

time_0

minimal exchange control

time_t

chosen time point

time_100

maximal exchange control

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_uptake calculates deuterium uptake (in different forms) for all of the peptides in given protein in given state based on supplied parameters: `time_0`, `time_100` and `time_t`. All four variants (fractiona) 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

read_hdx create_uptake_dataset calculate_confidence_limit_values add_stat_dependency

Examples

head(calculate_state_uptake(alpha_dat))
#>     Protein    Sequence Exposure Start End       State MaxUptake Modification
#> 1 db_eEF1Ba GFGDLKSPAGL        1     1  11 ALPHA_Gamma         9           NA
#> 2 db_eEF1Ba  FGDLKSPAGL        1     2  11 ALPHA_Gamma         8           NA
#> 3 db_eEF1Ba   GDLKSPAGL        1     3  11 ALPHA_Gamma         7           NA
#> 4 db_eEF1Ba      LKSPAG        1     5  10 ALPHA_Gamma         4           NA
#> 5 db_eEF1Ba     LKSPAGL        1     5  11 ALPHA_Gamma         5           NA
#> 6 db_eEF1Ba      AGLQVL        1     9  14 ALPHA_Gamma         5           NA
#>   frac_deut_uptake err_frac_deut_uptake deut_uptake err_deut_uptake
#> 1         31.26434            0.9842724   1.1779414      0.03520201
#> 2         55.16138            1.8959005   1.2928773      0.04425269
#> 3         55.03468            1.6368399   1.3274782      0.04011971
#> 4         49.78063            2.2253434   0.8577247      0.03897489
#> 5         49.11009            1.4982868   0.9622390      0.02979938
#> 6         20.49408            1.7389609   0.6691550      0.06028457
#>   theo_frac_deut_uptake err_theo_frac_deut_uptake theo_deut_uptake
#> 1             31.772784                 0.4298208        2.5923222
#> 2             44.516990                 0.5694457        3.2285460
#> 3             48.081013                 0.5628045        3.0511450
#> 4             34.926328                 1.0487918        1.2664969
#> 5             37.110129                 0.6431995        1.6821072
#> 6              5.666351                 1.0629184        0.2568412
#>   err_theo_deut_uptake Med_Sequence
#> 1           0.03506882          6.0
#> 2           0.04129842          6.5
#> 3           0.03571469          7.0
#> 4           0.03803124          7.5
#> 5           0.02915459          8.0
#> 6           0.04817937         11.5