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Create uptake dataset for chosen state

create_state_uptake_dataset.Rd

Calculates deuterium uptake values for one biological state.

Usage

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

Arguments

dat

data imported by the read_hdx function.

protein

chosen protein.

state

biological state 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

The function create_uptake_dataset generates a dataset with deuterium uptake values in different forms. For each peptide in chosen protein in chosen state 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 data can be presented in a form of comparison plot, butterfly plot or chiclet plot.

See also

read_hdx calculate_state_uptake

Examples

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