Create differential dataset with statistical validity
create_p_diff_uptake_dataset_with_confidence.RdCreate differential dataset with statistical validity
Usage
create_p_diff_uptake_dataset_with_confidence(
p_diff_uptake_dat,
houde_interval = NULL,
houde_interval_times = NULL,
theoretical = FALSE,
fractional = FALSE
)Arguments
- p_diff_uptake_dat
differential uptake data alongside the P-value as calculated by
create_p_diff_uptake_dataset- houde_interval
interval value, as calculated by
calculate_confidence_limit_values- houde_interval_times
specified time points to be used in calculation
- theoretical
logical, determines if values are theoretical- fractional
logical, determines if values are fractional
Value
a data.frame object.
Examples
p_diff_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat)
p_diff_uptake_dat_confidence <- create_p_diff_uptake_dataset_with_confidence(p_diff_uptake_dat)
head(p_diff_uptake_dat_confidence)
#> Protein Sequence Start End Exposure Modification ID MaxUptake
#> 1 db_eEF1Ba GFGDLKSPAGL 1 11 0.167 NA 1 9
#> 2 db_eEF1Ba GFGDLKSPAGL 1 11 1.000 NA 1 9
#> 3 db_eEF1Ba GFGDLKSPAGL 1 11 5.000 NA 1 9
#> 4 db_eEF1Ba GFGDLKSPAGL 1 11 25.000 NA 1 9
#> 5 db_eEF1Ba GFGDLKSPAGL 1 11 150.000 NA 1 9
#> 6 db_eEF1Ba GFGDLKSPAGL 1 11 1440.000 NA 1 9
#> 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 P_value log_p_value valid
#> 1 0.07447260 0.02076239 0.065344248 2.7280859 FALSE
#> 2 0.43164420 0.03913032 0.001789245 6.3259618 TRUE
#> 3 0.39465576 0.05731850 NA NA NA
#> 4 0.53044168 0.10681109 0.023503782 3.7505939 FALSE
#> 5 0.06695263 0.09457525 0.530754368 0.6334559 FALSE
#> 6 0.02510190 0.05514572 0.672642212 0.3965417 FALSE