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Calculate differential uptake

calculate_diff_uptake.Rd

Calculates differential deuterium uptake between two selected biological states.

Usage

calculate_diff_uptake(
  dat,
  protein = unique(dat[["Protein"]][1]),
  states = unique(dat[["State"]])[1:2],
  time_0 = min(dat[["Exposure"]]),
  time_t = unique(dat[["Exposure"]])[3],
  time_100 = max(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat

data imported by the read_hdx function.

protein

chosen protein.

states

vector of two states for chosen protein. Order is important, as the deuterium uptake difference is calculated as state_1 - state_2.

time_0

minimal exchange control time point of measurement [min].

time_t

time point of the measurement for which the calculations are done [min].

time_100

maximal exchange control time point of measurement [min].

deut_part

deuterium percentage in solution used in experiment, value from range [0, 1].

Value

a data.frame object.

Details

Function calculate_diff_uptake calculates differential values based on provided criteria for peptides for chosen protein in selected states. The methods of calculation of deuterium uptake difference, fractional deuterium uptake difference with respect to minimal/maximal exchange controls or theoretical tabular values are thoroughly described in the `Data processing` article, as well as law of propagation of uncertainty, used to calculate uncertainty.

See also

read_hdx calculate_state_uptake

Examples

diff_dat <- calculate_diff_uptake(alpha_dat)
head(diff_dat)
#>     Protein Start End MaxUptake Med_Sequence    Sequence Exposure Modification
#> 1 db_eEF1Ba     1  11         9          6.0 GFGDLKSPAGL        1           NA
#> 2 db_eEF1Ba     2  11         8          6.5  FGDLKSPAGL        1           NA
#> 3 db_eEF1Ba     3  11         7          7.0   GDLKSPAGL        1           NA
#> 4 db_eEF1Ba     5  10         4          7.5      LKSPAG        1           NA
#> 5 db_eEF1Ba     5  11         5          8.0     LKSPAGL        1           NA
#> 6 db_eEF1Ba     9  14         5         11.5      AGLQVL        1           NA
#>   diff_frac_deut_uptake err_diff_frac_deut_uptake diff_deut_uptake
#> 1              7.739209                 0.8730847        0.4316442
#> 2              9.485526                 1.2148237        0.4106231
#> 3              9.954930                 1.4161479        0.4464222
#> 4             11.304104                 1.6267043        0.3126567
#> 5              7.422823                 2.0256317        0.2317277
#> 6             10.155951                 1.4919668        0.3559280
#>   err_diff_deut_uptake diff_theo_frac_deut_uptake
#> 1           0.03913032                   5.290445
#> 2           0.04516371                   5.661900
#> 3           0.05757340                   7.034877
#> 4           0.04479526                   8.622168
#> 5           0.06318272                   5.112304
#> 6           0.05074159                   7.852374
#>   err_diff_theo_frac_deut_uptake diff_theo_deut_uptake
#> 1                      0.4796005             0.4316442
#> 2                      0.6227424             0.4106231
#> 3                      0.9072618             0.4464222
#> 4                      1.2353239             0.3126567
#> 5                      1.3939177             0.2317277
#> 6                      1.1194452             0.3559280
#>   err_diff_theo_deut_uptake ID
#> 1                0.03913032  1
#> 2                0.04516371  2
#> 3                0.05757340  3
#> 4                0.04479526  4
#> 5                0.06318272  5
#> 6                0.05074159  6