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Experiment quality control

create_quality_control_dataset.Rd

Checks how the uncertainty changes in a function of maximal exchange control time of measurement.

Usage

create_quality_control_dataset(
  dat,
  protein = dat[["Protein"]][1],
  state_1 = unique(dat[["State"]])[1],
  state_2 = unique(dat[["State"]])[2],
  time_t = unique(dat[["Exposure"]])[2],
  time_0 = min(dat[["Exposure"]]),
  deut_part = 0.9
)

Arguments

dat

data imported by the read_hdx function.

protein

chosen protein.

state_1

first biological state.

state_2

second biological state.

time_t

time point of the measurement for which the calculations are done.

time_0

minimal exchange control time point of measurement.

deut_part

deuterium percentage in solution used in experiment, value from range [0, 1].

Value

data.frame object with mean uncertainty per different `time_100` value. The values are shown as percentages.

Details

The function calculates mean uncertainty of all peptides and its uncertainty (standard error) based on given `time_0` and `time_t` as a function of `time_100`. Both theoretical and experimental results for each state and their difference are supplied for comparison but only experimental calculations depends on `time_100` variable. The results are either in form of fractional or absolute values depending on the `fractional` parameter supplied by the user. This data can be useful for general overview of the experiment and analyse of the chosen time parameters.

See also

read_hdx calculate_state_uptake plot_quality_control show_quality_control_data

Examples

create_quality_control_dataset(alpha_dat)    
#>   time_100 avg_err_state_1 sd_err_state_1 avg_err_state_2 sd_err_state_2
#> 1        1       3.4002155      8.8708525       34.521192     278.098101
#> 2        5       3.9326935     20.4036730        7.166776      34.925573
#> 3       25       1.6572207      3.0179749        4.932370      18.417678
#> 4      150       1.2427509      1.2804898        1.572092       1.822506
#> 5     1440       0.7168737      0.5591136        1.066821       1.099889
#>    avg_diff    sd_diff
#> 1 35.942627 278.078773
#> 2  9.801873  40.082153
#> 3  5.446570  18.593114
#> 4  2.117561   2.118622
#> 5  1.349636   1.162431