add_stat_dependency.RdReturns relation with confidence limits for each peptide.
add_stat_dependency( calc_dat, confidence_limit = 0.98, theoretical = FALSE, relative = TRUE )
| calc_dat | processed data from DynamX file - using |
|---|---|
| confidence_limit | confidence limit chosen by user - from range [0, 1]. |
| theoretical | logical value to determine if the plot is theoretical or not. |
| relative | logical value to determine if values are relative or absolute. |
calc_dat extended by column specifying if given peptide is relevant in given confidence limit. The value of the confidence limit is added as an attribute - as well as parameters used to calculate (theoretical/relative)
...
#load example data dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv")) # prepate dataset for states `CD160` and `CD160_HVEM` in given time parameters calc_dat <- prepare_dataset(dat, in_state_first = "CD160_0.001", chosen_state_first = "CD160_1", out_state_first = "CD160_1440", in_state_second = "CD160_HVEM_0.001", chosen_state_second = "CD160_HVEM_1", out_state_second = "CD160_HVEM_1440") # add calculated confidence limits for prepared data add_stat_dependency(calc_dat, confidence_limit = 0.98, theoretical = FALSE, relative = TRUE)#> # A tibble: 41 x 29 #> Sequence Start End Med_Sequence frac_exch_state~ err_frac_exch_s~ #> <chr> <int> <int> <dbl> <dbl> <dbl> #> 1 INITSSA~ 1 15 8 0.842 0.00173 #> 2 LICTVW 16 21 18.5 0.320 0.00469 #> 3 LICTVWH~ 16 29 22.5 0.680 0.00226 #> 4 ICTVWHK~ 17 29 23 0.733 0.00163 #> 5 FVVFL 30 34 32 0.250 0.00256 #> 6 LCKDRSG~ 34 48 41 0.941 0.00107 #> 7 LCKDRSG~ 34 49 41.5 0.922 0.000863 #> 8 LCKDRSG~ 34 51 42.5 0.883 0.000639 #> 9 LCKDRSG~ 34 69 51.5 0.902 0.00100 #> 10 CKDRSGD~ 35 48 41.5 0.940 0.00170 #> # ... with 31 more rows, and 23 more variables: frac_exch_state_2 <dbl>, #> # err_frac_exch_state_2 <dbl>, diff_frac_exch <dbl>, err_frac_exch <dbl>, #> # abs_frac_exch_state_1 <dbl>, err_abs_frac_exch_state_1 <dbl>, #> # abs_frac_exch_state_2 <dbl>, err_abs_frac_exch_state_2 <dbl>, #> # abs_diff_frac_exch <dbl>, err_abs_diff_frac_exch <dbl>, #> # avg_theo_in_time_1 <dbl>, err_avg_theo_in_time_1 <dbl>, #> # avg_theo_in_time_2 <dbl>, err_avg_theo_in_time_2 <dbl>, #> # diff_theo_frac_exch <dbl>, err_diff_theo_frac_exch <dbl>, #> # abs_avg_theo_in_time_1 <dbl>, err_abs_avg_theo_in_time_1 <dbl>, #> # abs_avg_theo_in_time_2 <dbl>, err_abs_avg_theo_in_time_2 <dbl>, #> # abs_diff_theo_frac_exch <dbl>, err_abs_diff_theo_frac_exch <dbl>, #> # valid_at_0.98 <lgl>