Skip to contents

Calculate Area Under the Curve

calculate_auc.Rd

Calculates area under the deuterium uptake curve

Usage

calculate_auc(
  uptake_dat,
  protein = uptake_dat[["Protein"]][1],
  state = uptake_dat[["State"]][1],
  preserve_values = FALSE
)

Arguments

uptake_dat

data with deuterium uptake values, calculated e.q. by create_uptake_dataset

protein

chosen protein

state

state included in calculations

preserve_values

indicator if the original columns form uptake_dat should be preserve in the result

Value

a data.frame object

Details

The AUC is calculated on the data normalized to unit square by division by maximum values of exposure time and deuterium uptake, respectively.

See also

read_hdx create_uptake_dataset

Examples

uptake_dat <- create_uptake_dataset(alpha_dat)
head(calculate_auc(uptake_dat))
#>     Protein    Sequence Start End       State Modification       auc
#> 1 db_eEF1Ba GFGDLKSPAGL     1  11 ALPHA_Gamma           NA 0.9973726
#> 2 db_eEF1Ba  FGDLKSPAGL     2  11 ALPHA_Gamma           NA 0.9993199
#> 3 db_eEF1Ba   GDLKSPAGL     3  11 ALPHA_Gamma           NA 1.0119067
#> 4 db_eEF1Ba      LKSPAG     5  10 ALPHA_Gamma           NA 0.9991318
#> 5 db_eEF1Ba     LKSPAGL     5  11 ALPHA_Gamma           NA 0.9991318
#> 6 db_eEF1Ba      AGLQVL     9  14 ALPHA_Gamma           NA 0.8587529