Create fits for all the peptides
create_fit_dataset.RdThis is a wrapper function for get_fit_results, but for multiple peptides at the same time. First, it creates a peptide list from the supplied deuterium uptake data, and calls the fitting function for each, to create full dataset.
Usage
create_fit_dataset(
kin_dat,
fit_k_params,
control = list(maxiter = 1000, scale = "levenberg"),
trace = F,
fractional = F,
workflow = 321
)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 2.5918362 5.870020
#> 2 2 db_eEF1Ba ALPHA_Gamma FGDLKSPAGL 2 11 8 2.6495960 7.234888
#> 3 3 db_eEF1Ba ALPHA_Gamma GDLKSPAGL 3 11 7 2.7013593 7.507887
#> 4 4 db_eEF1Ba ALPHA_Gamma LKSPAG 5 10 4 1.3953257 6.717443
#> 5 5 db_eEF1Ba ALPHA_Gamma LKSPAGL 5 11 5 1.5263186 6.866652
#> 6 6 db_eEF1Ba ALPHA_Gamma AGLQVL 9 14 5 0.3919301 2.603586
#> n_2 k_2 n_3 k_3 rss bic class_name
#> 1 1.747477 0.1471729 1.093423 0.0178303882 1.972152e-31 -405.38705 NA
#> 2 1.671734 0.4732856 0.000000 0.0000000000 8.022972e-03 -13.71718 NA
#> 3 1.805400 0.4905359 0.000000 0.0000000000 2.168912e-03 -21.56567 NA
#> 4 1.356225 0.4680721 0.000000 0.0000000000 1.133739e-03 -25.45790 NA
#> 5 1.585653 0.4754323 0.000000 0.0000000000 1.075759e-03 -25.77287 NA
#> 6 2.271788 0.2740198 5.000000 0.0001269509 5.257664e-03 -12.66939 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 0.2144616 3 #0D4CA6