Create fits for the whole peptide pool
create_fit_dataset.RdThis function calls the fitting function get_fit_results
for each peptide in supplied kin_dat creating the dataset for whole
peptide pool.
Usage
create_fit_dataset(
kin_dat,
fit_k_params,
control = list(maxiter = 1000, scale = "levenberg"),
trace = FALSE,
fractional = FALSE,
omit_t_100 = FALSE,
workflow = 321
)Arguments
- kin_dat
calculated uptake data for one biological state, result of e.q.
prepare_kin_dat- fit_k_params
boundaries for exchange groups, example in prepare_kin_dat
- control
control options for the fitting process, example in
get_example_control- trace
logical, indicator if fitting trace is to be displayed
- fractional
logical, indicator if normalized values are used in the fitting process
- workflow
workflow type, options: 321, 31, 21, indicating the types of functions used in fitting process
Examples
kin_dat <- prepare_kin_dat(alpha_dat)
fit_k_params <- get_example_fit_k_params()
head(create_fit_dataset(kin_dat, fit_k_params))
#> id Protein State sequence start end max_uptake n_1 k_1
#> 1 1 db_eEF1Ba ALPHA_Gamma GFGDLKSPAGL 1 11 9 2.591836 5.870020
#> 2 2 db_eEF1Ba ALPHA_Gamma FGDLKSPAGL 2 11 8 2.649596 7.234888
#> 3 3 db_eEF1Ba ALPHA_Gamma GDLKSPAGL 3 11 7 2.701359 7.507887
#> 4 4 db_eEF1Ba ALPHA_Gamma LKSPAG 5 10 4 1.395326 6.717443
#> 5 5 db_eEF1Ba ALPHA_Gamma LKSPAGL 5 11 5 1.526319 6.866652
#> 6 6 db_eEF1Ba ALPHA_Gamma AGLQVL 9 14 5 1.000000 1.000000
#> n_2 k_2 n_3 k_3 rss bic class_name
#> 1 1.747477 0.1471729 1.093423 0.0178303882 1.183291e-30 -394.636496 NA
#> 2 1.671734 0.4732856 0.000000 0.0000000000 8.022972e-03 -13.717175 NA
#> 3 1.805400 0.4905359 0.000000 0.0000000000 2.168912e-03 -21.565674 NA
#> 4 1.356225 0.4680721 0.000000 0.0000000000 1.133739e-03 -25.457904 NA
#> 5 1.585653 0.4754323 0.000000 0.0000000000 1.075759e-03 -25.772868 NA
#> 6 1.660464 0.2151596 1.783585 0.0004384549 1.059401e-02 -8.465776 NA
#> k_est fitted color
#> 1 2.8513818 3 #7A5233
#> 2 4.6191186 2 #9C6300
#> 3 4.6967479 2 #996600
#> 4 3.6371609 2 #817E00
#> 5 3.6101125 2 #7D8200
#> 6 0.3055877 3 #395F66