Skip to contents

Back exchange estimation

calculate_back_exchange.Rd

Calculates back-exchange for a state

Usage

calculate_back_exchange(
  dat,
  protein = dat[["Protein"]][1],
  states = unique(dat[["State"]]),
  time_100 = max(dat[["Exposure"]])
)

Arguments

dat

data imported by the read_hdx function

protein

selected protein

states

selected biological states for given protein

time_100

time point of measurement for fully deuterated sample

Value

a data.frame object

Details

Back-exchange is a reverse exchange phenomenon, important to acknowledge when working with HDX data. This function calculates back-exchange values for one biological state of the selected protein. For visualization of back-exchange data use plot_coverage_heatmap with displayed value specified as `back-exchange`. For the definition of back-exchange see the `vignette("datafiles")`.

See also

read_hdx plot_coverage_heatmap

Examples

head(calculate_back_exchange(alpha_dat))
#>     Protein Start End       State    Sequence Modification back_exchange
#> 1 db_eEF1Ba     1  11 ALPHA_Gamma GFGDLKSPAGL           NA      36.48605
#> 2 db_eEF1Ba     2  11 ALPHA_Gamma  FGDLKSPAGL           NA      40.99218
#> 3 db_eEF1Ba     3  11 ALPHA_Gamma   GDLKSPAGL           NA      34.82752
#> 4 db_eEF1Ba     5  10 ALPHA_Gamma      LKSPAG           NA      41.21163
#> 5 db_eEF1Ba     5  11 ALPHA_Gamma     LKSPAGL           NA      40.89189
#> 6 db_eEF1Ba     9  14 ALPHA_Gamma      AGLQVL           NA      37.06240
#>   err_back_exchange
#> 1        0.46550621
#> 2        0.36925011
#> 3        0.42056545
#> 4        0.12960786
#> 5        0.06323022
#> 6        0.91755764