Read HDX-MS data file
read_hdx.Rd
Import HDX-MS datafile and validate its content
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
.
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