Read HDX-MS data file

Imports data from a HDX-MS file and validates its content.

read_hdx(filename)

Arguments

filename	a file supplied by the user. Formats allowed: .csv, .xlsx and .xls.

Value

dat - a data.frame with validated content.

Details

First version accepts files produced by DynamX 3.0 and 2.0 in `cluster data` format. The function checks if all necessary columns are provided in correct format. The file must include at least two repetitions of the measurement for the uncertainty to be calculated.

See also

calculate_kinetics calculate_state_deuteration plot_coverage plot_position_frequency prepare_dataset quality_control reconstruct_sequence

Examples

# read example data
head(read_hdx(system.file(package = "HaDeX", 
                     "HaDeX/data/KD_180110_CD160_HVEM.csv")))
#>     Protein Start End        Sequence Modification Fragment MaxUptake      MHP
#> 1: db_CD160     1  15 INITSSASQEGTRLN           NA       NA        14 1590.808
#> 2: db_CD160     1  15 INITSSASQEGTRLN           NA       NA        14 1590.808
#> 3: db_CD160     1  15 INITSSASQEGTRLN           NA       NA        14 1590.808
#> 4: db_CD160     1  15 INITSSASQEGTRLN           NA       NA        14 1590.808
#> 5: db_CD160     1  15 INITSSASQEGTRLN           NA       NA        14 1590.808
#> 6: db_CD160     1  15 INITSSASQEGTRLN           NA       NA        14 1590.808
#>    State Exposure                    File z       RT  Inten    Center
#> 1: CD160    0.000 KD_160527_CD160_sekw_05 1 3.232479   6592 1591.2584
#> 2: CD160    0.000 KD_160527_CD160_sekw_05 2 3.238079 394066  796.3552
#> 3: CD160    0.000 KD_160527_CD160_sekw_05 3 3.238759 173526  531.2633
#> 4: CD160    0.001   KD_160527_CD160_IN_01 2 3.258598 232221  796.3634
#> 5: CD160    0.001   KD_160527_CD160_IN_01 3 3.256844 110675  531.2849
#> 6: CD160    0.167  KD_160530_CD160_10s_01 2 3.262774  99894  800.3610