read_hdx: Read HDX-MS data file

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Read HDX-MS data file

Description

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.

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.

Value

a data.frame object

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)

HaDeX2 documentation built on Feb. 9, 2026, 5:07 p.m.