Flag outlier scans — orbi_flag

The function orbi_flag_outliers() 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 "filename", "block", "segment" and "injection" (if these columns exist), in addition to any groupings already defined before calling this function using dplyr's group_by(). It restores the original groupings in the returned data frame.

Usage

orbi_flag_outliers(dataset, agc_fold_cutoff = NA_real_, agc_window = c())

Arguments

dataset: Simplified IsoX dataset to have outliers flagged
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.

Value

A data frame 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.

Details

Function is intended to flag scans that are outliers.

The input dataset is expected to have at least these 8 columns: filename, scan.no, time.min, compound, isotopocule, ions.incremental, tic, it.ms.

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
#> ✔ [62ms] 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
#> ✔ [44ms] orbi_flag_outliers() flagged 24/1290 scans (1.9%) 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