Generate differential dataset
create_diff_uptake_dataset.RdCalculates differential deuterium uptake values between two states.
Arguments
- dat
data imported by the
read_hdxfunction.- protein
chosen protein.
- state_1
biological state for chosen protein. From this state values the second state values are subtracted to get the deuterium uptake difference.
- state_2
biological state for chosen protein. This state values are subtracted from the first state values to get the deuterium uptake difference.
- 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_diff_uptake_dataset
generates a dataset with differential values between given biological states
(state_1 - state_2). For each peptide of chosen protein for time points of
measurement between minimal and maximal control time points of measurement
deuterium uptake difference, fractional deuterium uptake difference 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.
Function output can be visualized as a differential (Woods) plot, butterfly
differential plot or chiclet differential plot.
Examples
diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
head(diff_uptake_dat)
#> ID Exposure Protein Sequence Start End MaxUptake Modification
#> 1 1 0.167 db_eEF1Ba GFGDLKSPAGL 1 11 9 NA
#> 2 1 1.000 db_eEF1Ba GFGDLKSPAGL 1 11 9 NA
#> 3 1 5.000 db_eEF1Ba GFGDLKSPAGL 1 11 9 NA
#> 4 1 25.000 db_eEF1Ba GFGDLKSPAGL 1 11 9 NA
#> 5 1 150.000 db_eEF1Ba GFGDLKSPAGL 1 11 9 NA
#> 6 1 1440.000 db_eEF1Ba GFGDLKSPAGL 1 11 9 NA
#> Med_Sequence State_1 frac_deut_uptake_1 err_frac_deut_uptake_1
#> 1 6 ALPHA_Gamma 30.648518 0.22154053
#> 2 6 ALPHA_Gamma 52.330800 0.74197387
#> 3 6 ALPHA_Gamma 66.179800 1.15204366
#> 4 6 ALPHA_Gamma 86.300338 1.46322512
#> 5 6 ALPHA_Gamma 98.612529 1.63494174
#> 6 6 ALPHA_Gamma 1.434621 0.01002946
#> deut_uptake_1 err_deut_uptake_1 theo_frac_deut_uptake_1
#> 1 1.665053 0.003059254 17.33535
#> 2 2.842995 0.035068821 31.77278
#> 3 3.595375 0.057318502 40.99432
#> 4 4.688471 0.072421134 54.39185
#> 5 5.357359 0.080539467 62.59008
#> 6 5.432737 0.037980370 63.51395
#> err_theo_frac_deut_uptake_1 theo_deut_uptake_1 err_theo_deut_uptake_1
#> 1 0.03749574 1.414381 0.003059254
#> 2 0.42982083 2.592322 0.035068821
#> 3 0.70252393 3.344702 0.057318502
#> 4 0.88762927 4.437798 0.072421134
#> 5 0.98713157 5.106687 0.080539467
#> 6 0.46550621 5.182064 0.037980370
#> State_2 frac_deut_uptake_2 err_frac_deut_uptake_2 deut_uptake_2
#> 1 ALPHA_beta_gamma 29.413612 0.43761622 1.590581
#> 2 ALPHA_beta_gamma 44.591592 0.46016476 2.411351
#> 3 ALPHA_beta_gamma 59.188881 0.43761754 3.200719
#> 4 ALPHA_beta_gamma 76.891814 1.55917136 4.158029
#> 5 ALPHA_beta_gamma 97.832169 1.16778379 5.290407
#> 6 ALPHA_beta_gamma 1.427992 0.01055797 5.407635
#> err_deut_uptake_2 theo_frac_deut_uptake_2 err_theo_frac_deut_uptake_2
#> 1 0.02053577 16.42258 0.2516966
#> 2 0.01735971 26.48234 0.2127692
#> 3 0.00000000 36.15723 0.0000000
#> 4 0.07850979 47.89049 0.9622549
#> 5 0.04957693 61.76948 0.6076394
#> 6 0.03998177 63.20629 0.4900363
#> theo_deut_uptake_2 err_theo_deut_uptake_2 diff_frac_deut_uptake
#> 1 1.339908 0.02053577 1.234906456
#> 2 2.160678 0.01735971 7.739208705
#> 3 2.950046 0.00000000 6.990918595
#> 4 3.907356 0.07850979 9.408523973
#> 5 5.039734 0.04957693 0.780359881
#> 6 5.156963 0.03998177 0.006628648
#> err_diff_frac_deut_uptake diff_deut_uptake err_diff_deut_uptake
#> 1 0.49049787 0.07447260 0.02076239
#> 2 0.87308467 0.43164420 0.03913032
#> 3 1.23236102 0.39465576 0.05731850
#> 4 2.13823364 0.53044168 0.10681109
#> 5 2.00916736 0.06695263 0.09457525
#> 6 0.01456231 0.02510190 0.05514572
#> diff_theo_frac_deut_uptake err_diff_theo_frac_deut_uptake
#> 1 0.9127730 0.2544742
#> 2 5.2904450 0.4796005
#> 3 4.8370964 0.7025239
#> 4 6.5013558 1.3091295
#> 5 0.8206046 1.1591611
#> 6 0.3076613 0.6758932
#> diff_theo_deut_uptake err_diff_theo_deut_uptake
#> 1 0.07447260 0.02076239
#> 2 0.43164420 0.03913032
#> 3 0.39465576 0.05731850
#> 4 0.53044168 0.10681109
#> 5 0.06695263 0.09457525
#> 6 0.02510190 0.05514572