Calculate differential uptake
calculate_diff_uptake.Rd
Calculates differential deuterim uptake between two selected biological states.
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.
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