Set peak table from vendor data

Source: R/peak_table.R

Set the peak table from vendor data in each iso_file. Only the vendor data table columns that do exist in a file will be used, so this function can set peak table information across a variety of data files without errors. Provides a detailed info message about the columns that are used.

iso_set_peak_table_from_vendor_data_table(
  iso_files,
  direct_rename = c(),
  regex_rename = c(),
  quiet = default(quiet)
)

iso_set_peak_table_automatically_from_vendor_data_table(
  iso_files,
  quiet = default(quiet)
)

iso_set_peak_table_from_isodat_vendor_data_table(
  iso_files,
  quiet = default(quiet)
)

Arguments

direct_rename

select which columns to select and rename directly from the vendor data table. Must be a named vector with the values the vendor data table column names and the names the corresponding peak table column names.
regex_rename

select columns by regular expression and rename using str_replace. Must be a named vector with the values the regular expression to find vendor data table columns and the names the replacement expression for the correponding peak table column names.

Details

iso_set_peak_table_automatically_from_vendor_data_table is the easiest way to set peak tables from vendor data because it will simply look at the file extension and decide which software specific function to use (e.g. iso_set_peak_table_from_isodat_vendor_data_table) for any Isodat files.

iso_set_peak_table_from_isodat_vendor_data_table provides specialized functionality to set peak table information from an Isodat vendor data tables. For compatibility with all downstream isoprocessor calculations, the resulting peak table has a very specific set of columns which are listed below. Mapping for Isodat data tables:

  • peak_nr: "Nr."

  • is_ref: "Is Ref.?"

  • rt_start: "Start"

  • rt: "Rt"

  • rt_end: "End"

  • ampX: "Ampl X"

  • bgrdX_start: "BGD X"

  • bgrdX_end: "BGD X" (Isodat only reports a single background amplitude)

  • areaX: "rIntensity X" (recorded intensities)

  • rX/Y: "rR X/Y" (recorded ratios)

  • rX/Y_ref: extrapolated reference ratio at the peak (not available from Isodat peak table)

  • rdX/Y: "rd X/Y" (recorded delta -> rX/Y / rX/Y_ref - 1, not shifted for true isotopic value of the ref)

  • dX/Y: "d X/Y" (delta frame shifted wrt to the true isotopic value of the ref; note that if this is a single element delta keeps just the numerator with the element symbol to fit conventional naming, e.g. d13C or d18O; whereas for a molecule omits the formula and keeps the mass ratios, e.g. d45/44)

  • atX: "AT

See also

Other peak table functions: iso_get_peak_table(), iso_mutate_peak_table(), iso_set_peak_table()