Skip to contents

orbi_define_basepeak() sets one isotopocule in the data frame as the base peak (ratio denominator) and calculates the instantaneous isotope ratios against it.


orbi_define_basepeak(dataset, basepeak_def)



A tibble from a IsoX output. Needs to contain columns for filename, compound,, isotopocule, and ions.incremental.


The isotopocule that gets defined as base peak, i.e. the denominator to calculate ratios


Input data frame without the rows of the basepeak isotopocule and instead three new columns called basepeak, basepeak_ions, and ratio holding the basepeak information and the isotope ratios vs. the base peak


fpath <- system.file("extdata", "testfile_flow.isox", package = "isoorbi")
df <- orbi_read_isox(file = fpath) |>
  orbi_simplify_isox() |>
  orbi_define_basepeak(basepeak_def = "M0")
#> orbi_read_isox() is loading .isox data from 1 file(s)...
#> - loaded 6449 peaks for 1 compounds (HSO4-) with 5 isotopocules (M0, 33S,
#>    17O, 34S, 18O) from testfile_flow.isox in 0.02 seconds.
#> orbi_simplify_isox() will keep only columns 'filepath', 'filename',
#>    '', 'time.min', 'compound', 'isotopocule', 'ions.incremental',
#>    'tic', ''...
#>    ...complete in 0.00 seconds.
#> orbi_define_basepeak() is setting the 'M0' isotopocule as the ratio
#>    denominator...
#>    ...set base peak and calculated 5159 ratios for 4 isotopocules/base peak
#>    (33S, 17O, 34S, 18O) in 0.06 seconds.