Skip to contents

Read HDX-MS data file

read_hdx.Rd

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 = "HaDeX2", 
                     "HaDeX/data/alpha.csv"))
head(dat)
#>      Protein Start   End    Sequence Modification MaxUptake      MHP
#>       <char> <int> <int>      <char>       <lgcl>     <int>    <num>
#> 1: db_eEF1Ba     1    11 GFGDLKSPAGL           NA         9 1061.563
#> 2: db_eEF1Ba     1    11 GFGDLKSPAGL           NA         9 1061.563
#> 3: db_eEF1Ba     1    11 GFGDLKSPAGL           NA         9 1061.563
#> 4: db_eEF1Ba     1    11 GFGDLKSPAGL           NA         9 1061.563
#> 5: db_eEF1Ba     1    11 GFGDLKSPAGL           NA         9 1061.563
#> 6: db_eEF1Ba     1    11 GFGDLKSPAGL           NA         9 1061.563
#>          State Exposure                              File     z  Inten
#>         <char>    <num>                            <char> <int>  <int>
#> 1: ALPHA_Gamma    0.000 Tania_161112_eEF1Ba_KSCN_IMS_seq1     1 138844
#> 2: ALPHA_Gamma    0.000 Tania_161112_eEF1Ba_KSCN_IMS_seq1     2 728218
#> 3: ALPHA_Gamma    0.167  Tania_161109_1eEF1Bag_KSCN_10sec     1  41100
#> 4: ALPHA_Gamma    0.167  Tania_161109_1eEF1Bag_KSCN_10sec     2 393115
#> 5: ALPHA_Gamma    0.167  Tania_161109_2eEF1Bag_KSCN_10sec     1  46642
#> 6: ALPHA_Gamma    0.167  Tania_161109_2eEF1Bag_KSCN_10sec     2 466233
#>       Center
#>        <num>
#> 1: 1062.1913
#> 2:  531.6754
#> 3: 1064.0150
#> 4:  532.4975
#> 5: 1063.9682
#> 6:  532.4951