Calculates aggregated deuterium uptake for one time point
calculate_aggregated_uptake.RdFunction aggregates the deuterium uptake values from
peptide level into single-amino resolution using `weighted
approach` (definied in `vignette("datafiles"))`. For
visualization use plot_aggregated_uptake
Usage
calculate_aggregated_uptake(
kin_dat,
state = unique(kin_dat[["State"]])[1],
time_t
)Arguments
- kin_dat
single state uptake data, product of e.q.
create_uptake_dataset- state
state included in calculations
- time_t
chosen time point
Value
a data.frame object
Examples
dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv"))
#> [1] ""
kin_dat <- create_uptake_dataset(alpha_dat, states = "Alpha_KSCN")
head(create_aggregated_uptake_dataset(kin_dat))
#> position aa frac_deut_uptake err_frac_deut_uptake deut_uptake err_deut_uptake
#> 1 1 G 32.40425 1.088174 1.760438 0.06314206
#> 2 2 F 54.45759 1.401526 2.525757 0.03305064
#> 3 3 G 62.36775 1.754654 2.848953 0.02685878
#> 4 4 D 62.36775 1.754654 2.848953 0.02685878
#> 5 5 L 66.15272 2.366262 2.403291 0.01874680
#> 6 6 K 66.15272 2.366262 2.403291 0.01874680
#> theo_frac_deut_uptake err_theo_frac_deut_uptake theo_deut_uptake
#> 1 18.50443 0.7739003 1.509765
#> 2 31.75040 0.4152717 2.381605
#> 3 37.80716 0.3752152 2.627697
#> 4 37.80716 0.3752152 2.627697
#> 5 37.12189 0.3984766 2.004130
#> 6 37.12189 0.3984766 2.004130
#> err_theo_deut_uptake Exposure
#> 1 0.06314206 0.167
#> 2 0.03305064 0.167
#> 3 0.02685878 0.167
#> 4 0.02685878 0.167
#> 5 0.01874680 0.167
#> 6 0.01874680 0.167