Read HDX-MS data file

Import HDX-MS datafile and validate its content

Usage

read_hdx(filename, separator = ",")

Arguments

filename

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

separator

a value separating the columns.

Value

a data.frame object

Details

The function read_hdx generates a dataset read from the supplied datafile. The files produced by DynamX 3.0 or 2.0 in `cluster data` format and `tables` file from HDeXaminer are handled. Moreover, the data should include at least two replicates of the experiment to calculate the uncertainty of the measurement. For the files of HDeXaminer origin, the rows with no complete information (e.q. missing `Exp Cent` value) are removed. The `Confidence` column is preserved as the user should have impact on accepting rows based on their Confidence flag. Moreover, those files need action from the user - to confirm data processing (e.q. FD time point), choose accepted confidence values and make some change of the labels using update_hdexaminer_file function. For further information check the documentation. IMPORTANT! The files of HDeXaminer origin MUST be processed by hand or by update_hdexaminer_file function to fit the input of processing functions e.q. calculate_state_uptake or calculate_diff_uptake.

See also

update_hdexaminer_file create_control_dataset calculate_state_uptake

Examples

dat <- read_hdx(system.file(package = "HaDeX", 
                     "HaDeX/data/KD_180110_CD160_HVEM.csv"))
#> [1] ""
head(dat)
#>     Protein Start   End        Sequence Modification MaxUptake      MHP  State
#>      <char> <int> <int>          <char>       <lgcl>     <num>    <num> <char>
#> 1: db_CD160     1    15 INITSSASQEGTRLN           NA        14 1590.808  CD160
#> 2: db_CD160     1    15 INITSSASQEGTRLN           NA        14 1590.808  CD160
#> 3: db_CD160     1    15 INITSSASQEGTRLN           NA        14 1590.808  CD160
#> 4: db_CD160     1    15 INITSSASQEGTRLN           NA        14 1590.808  CD160
#> 5: db_CD160     1    15 INITSSASQEGTRLN           NA        14 1590.808  CD160
#> 6: db_CD160     1    15 INITSSASQEGTRLN           NA        14 1590.808  CD160
#>    Exposure                    File     z  Inten    Center
#>       <num>                  <char> <int>  <num>     <num>
#> 1:    0.000 KD_160527_CD160_sekw_05     1   6592 1591.2584
#> 2:    0.000 KD_160527_CD160_sekw_05     2 394066  796.3552
#> 3:    0.000 KD_160527_CD160_sekw_05     3 173526  531.2633
#> 4:    0.001   KD_160527_CD160_IN_01     2 232221  796.3634
#> 5:    0.001   KD_160527_CD160_IN_01     3 110675  531.2849
#> 6:    0.167  KD_160530_CD160_10s_01     2  99894  800.3610