Flag outlier scans

This function flags outliers using one of the different methods provided by the parameters (to use multiple, please call this function several times sequentially). Note that this function evaluates outliers within each "uidx", "filename", and "injection" (for those of the columns that exist), and additionally within each "block" and "segment" if by_block = TRUE. in addition to any groupings already defined before calling this function using dplyr's group_by(). It restores the original groupings in the returned datasert.

Usage

orbi_flag_outliers(
  dataset,
  agc_fold_cutoff = NA_real_,
  agc_window = c(),
  agc_absolute_cutoff = c(),
  by_block = TRUE
)

Arguments

dataset

An aggregated dataset or a data frame of peaks (i.e. works directly after orbi_identify_isotopocules() as well as with a tibble from orbi_get_data(peaks = everything()) or when reading from an IsoX file)

agc_fold_cutoff

flags scans with a fold cutoff based on the average number of ions in the Orbitrap analyzer. For example, agc_fold_cutoff = 2 flags scans that have more than 2 times, or less than 1/2 times the average. TIC multiplied by injection time serves as an estimate for the number of ions in the Orbitrap.

agc_window

flags scans with a critically low or high number of ions in the Orbitrap analyzer. Provide a vector with 2 numbers c(x,y) flagging the lowest x percent and highest y percent. TIC multiplied by injection time serves as an estimate for the number of ions in the Orbitrap.

agc_absolute_cutoff

flags scans with a number of ions in the Orbitrap analyzer outside of an absolute range. Provide a vector with 2 numbers c(x,y) flagging data below x and above y of the TIC multiplied by injection time (which serves as an estimate for the number of ions in the Orbitrap).

by_block

if the dataset has block and segment definitions, should the outlier flag be evaluated within each block+segment or globally? default is within each block+segment, switch to globally by turning by_block = FALSE

Value

same object as provided in dataset with new columns is_outlier and outlier_type (if they don't already exist) that flags outliers identified by the method and provides the type of outlier (e.g. "2 fold agc cutoff"), respectively.

Examples

fpath <- system.file("extdata", "testfile_flow.isox", package = "isoorbi")
df <-
  orbi_read_isox(file = fpath) |>
  orbi_simplify_isox() |>
  orbi_flag_outliers(agc_window = c(1,99))
#> ✔ [20ms] orbi_read_isox() loaded 6449 peaks for 1 compound (HSO4-) with 5
#> isotopocules (M0, 33S, 17O, 34S, and 18O) from testfile_flow.isox
#> ✔ [5ms] orbi_simplify_isox() kept columns filepath, filename, scan.no,
#> time.min, compound, isotopocule, ions.incremental, tic, and it.ms
#> ✔ [26ms] orbi_flag_outliers() flagged 30/1290 scans (2.3%) as outliers based on
#> AGC window (1% to 99%) cutoff, i.e. based on scans whose number of ions tic *
#> it.ms in the Orbitrap analyzer fall into the lowest (<1%) or highest (>99%)
#> quantiles, in 3 data groups (based on filename) → use orbi_plot_raw_data(y =
#> tic * it.ms) to visualize them