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Create dataset with control

create_control_dataset.Rd

This function adds selected experimental maximal exchange control as a measurement for all biological states.

Usage

create_control_dataset(
  dat,
  control_protein = dat[["Protein"]][1],
  control_state = dat[["State"]][1],
  control_exposure = max(dat[["Exposure"]])
)

Arguments

dat

data imported by the read_hdx function.

control_protein

maximal exchange control protein, from dat.

control_state

maximal exchange control state, from dat.

control_exposure

maximal exchange control exposure (time point of measurement), from dat.

Value

a data.frame object.

Details

Function create_control_dataset creates a dataset (similar to the output of read_hdx function), with maximal exchange control for all the states, based on provided parameters. The other functions are operating within a state, so the control is prepared for each state. The chosen maximal exchange control is distinguishable by the value `99999` in `Exposure` control.

See also

read_hdx calculate_state_uptake

Examples

head(create_control_dataset(alpha_dat))
#>     Protein Start End    Sequence Modification MaxUptake      MHP       State
#> 1 db_eEF1Ba     1  11 GFGDLKSPAGL           NA         9 1061.563 ALPHA_Gamma
#> 2 db_eEF1Ba     1  11 GFGDLKSPAGL           NA         9 1061.563 ALPHA_Gamma
#> 3 db_eEF1Ba     1  11 GFGDLKSPAGL           NA         9 1061.563 ALPHA_Gamma
#> 4 db_eEF1Ba     1  11 GFGDLKSPAGL           NA         9 1061.563 ALPHA_Gamma
#> 5 db_eEF1Ba     1  11 GFGDLKSPAGL           NA         9 1061.563 ALPHA_Gamma
#> 6 db_eEF1Ba     1  11 GFGDLKSPAGL           NA         9 1061.563 ALPHA_Gamma
#>   Exposure                              File z  Inten    Center
#> 1    0.000 Tania_161112_eEF1Ba_KSCN_IMS_seq1 1 138844 1062.1913
#> 2    0.000 Tania_161112_eEF1Ba_KSCN_IMS_seq1 2 728218  531.6754
#> 3    0.167  Tania_161109_1eEF1Bag_KSCN_10sec 1  41100 1064.0150
#> 4    0.167  Tania_161109_1eEF1Bag_KSCN_10sec 2 393115  532.4975
#> 5    0.167  Tania_161109_2eEF1Bag_KSCN_10sec 1  46642 1063.9682
#> 6    0.167  Tania_161109_2eEF1Bag_KSCN_10sec 2 466233  532.4951