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Create uptake dataset for multiple states

create_uptake_dataset.Rd

Calculates deuterium uptake values for selected biological states in multiple time points of measurements.

Usage

create_uptake_dataset(
  dat,
  protein = unique(dat[["Protein"]])[1],
  states = unique(dat[["State"]]),
  time_0 = min(dat[["Exposure"]]),
  time_100 = max(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat

data imported by the read_hdx function.

protein

chosen protein.

states

list of biological states for chosen protein.

time_0

minimal exchange control time point of measurement [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 create_uptake_dataset generates a dataset with deuterium uptake values in different forms. For each peptide in chosen protein in chosen states for time points of measurement between minimal and maximal control time points of measurement deuterium uptake, fractional deuterium uptake with respect to controls or theoretical tabular values are calculated, with combined and propagated uncertainty. Each peptide has an ID, based on its start position. This function is a wrapper for create_state_uptake_dataset but for multiple states. The output of this function can be presented in a form of comparison plot.

See also

read_hdx calculate_state_uptake create_state_uptake_dataset

Examples

dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv"))
#> [1] ""
uptake_dat <- create_uptake_dataset(dat, states = c("CD160", "CD160_HVEM"))
head(uptake_dat)
#>    Protein        Sequence Exposure Start End State MaxUptake Modification
#> 1 db_CD160 INITSSASQEGTRLN    0.001     1  15 CD160        14           NA
#> 2 db_CD160          LICTVW    0.001    16  21 CD160         5           NA
#> 3 db_CD160  LICTVWHKKEEAEG    0.001    16  29 CD160        13           NA
#> 4 db_CD160   ICTVWHKKEEAEG    0.001    17  29 CD160        12           NA
#> 5 db_CD160           FVVFL    0.001    30  34 CD160         4           NA
#> 6 db_CD160 LCKDRSGDCSPETSL    0.001    34  48 CD160        13           NA
#>   frac_deut_uptake err_frac_deut_uptake  deut_uptake err_deut_uptake
#> 1       0.36935223         0.0012947000  0.038605737               0
#> 2       0.03033506         0.0001481620  0.000888387               0
#> 3       0.34405201         0.0033762717  0.026403750               0
#> 4      -0.85967318         0.0058949102 -0.063096279               0
#> 5       1.31196247         0.0076786534  0.030796000               0
#> 6       0.23854825         0.0003776673  0.017958220               0
#>   theo_frac_deut_uptake err_theo_frac_deut_uptake theo_deut_uptake
#> 1            -0.4493436                         0      -0.05702927
#> 2           -10.9156277                         0      -0.49477747
#> 3             0.5814308                         0       0.06852240
#> 4            -0.7130478                         0      -0.07756952
#> 5           -16.5250744                         0      -0.59923147
#> 6             0.3030472                         0       0.03571452
#>   err_theo_deut_uptake Med_Sequence
#> 1                    0          8.0
#> 2                    0         18.5
#> 3                    0         22.5
#> 4                    0         23.0
#> 5                    0         32.0
#> 6                    0         41.0