update_hdexaminer_file: Update HDeXaminer datafile

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

Update HDeXaminer datafile

Description

Update data from HDeXaminer file

Usage

update_hdexaminer_file(
  dat,
  fd_time,
  old_protein_name = NULL,
  new_protein_name = NULL,
  old_state_name = NULL,
  new_state_name = NULL,
  confidence = c("High", "Medium")
)

Arguments

dat	data imported by the read_hdx function
fd_time	time point [min] for fully deuterated sample
old_protein_name	protein name to be changed
new_protein_name	new name for old_protein_name
old_state_name	state names to be changed
new_state_name	new names for old_state_name
confidence	vector of accepted confidence values (internal flag from HDeXaminer). By default only accepted values are 'Medium' and 'High', with 'Low' excluded

Details

The function update_hdexaminer_file changes the data read from HDeXaminer file. Data from HDeXaminer is condensed and automated data retrieving may be corrected by the user. The original file has a mark "FD" for fully deuterated data instead of numerical value for time point (provided in minutes) that is not consistent for workflow and not enough for precise data description. Moreover, the data about both protein and state is included in one column and for detailed information function update_hdexaminer_file allows to change them.

Value

a data.frame object

See Also

read_hdx calculate_kinetics plot_coverage plot_position_frequency reconstruct_sequence

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