Define the denominator for ratio calculation — orbi_define

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

Usage

orbi_define_basepeak(dataset, basepeak_def)

Arguments

dataset: A tibble from a IsoX output. Needs to contain columns for filename, compound, scan.no, isotopocule, and ions.incremental.
basepeak_def: The isotopocule that gets defined as base peak, i.e. the denominator to calculate ratios

Value

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

Examples

fpath <- system.file("extdata", "testfile_flow.isox", package = "isoorbi")
df <- orbi_read_isox(file = fpath) |>
  orbi_simplify_isox() |>
  orbi_define_basepeak(basepeak_def = "M0")
#> ✔ [20ms] orbi_read_isox() loaded 6449 peaks for 1 compound (HSO4-) with 5
#> isotopocules (M0, 33S, 17O, 34S, and 18O) from testfile_flow.isox
#> ✔ [61ms] orbi_read_isox() read .isox data from 1 file
#> ✔ [5ms] orbi_simplify_isox() kept columns filepath, filename, scan.no,
#> time.min, compound, isotopocule, ions.incremental, tic, and it.ms
#> ✔ [67ms] orbi_define_basepeak() set M0 as the ratio denominator and calculated
#> 5159 ratios for 4 isotopocules/base peak (33S, 17O, 34S, and 18O)