Update HDeXaminer datafile

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

Value

a data.frame object

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.

See also

read_hdx calculate_kinetics plot_coverage plot_position_frequency reconstruct_sequence

Examples

update_hdexaminer_file(alpha_dat)                      
#> Error in update_hdexaminer_file(alpha_dat): Supplied file is not of HDeXaminer origin.