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Basic generic data files filter

Source: R/read_isox.R
orbi_filter_files.Rd

This is a basic filter function for file names, compounds and time ranges. For filtering isotopocules, this function calls orbi_filter_isotopocules() internally (as of isoorbi version 1.5.0 orbi_filter_isotopocules() can also be used directly instead of via this function). Default value for all parameters is NULL, i.e. no filter is applied.

Usage

orbi_filter_files(
  dataset,
  filenames = NULL,
  compounds = NULL,
  isotopocules = NULL,
  time_min = NULL,
  time_max = NULL
)

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)

filenames

Vector of file names to keep, keeps all if set to NULL (the default)

compounds

Vector of compounds to keep, keeps all if set to NULL (the default)

isotopocules

Vector of isotopocules to keep, keeps all if set to NULL (the default)

time_min

Minimum retention time in minutes (time.min), no minimum if set to NULL (the default)

time_max

Maximum retention time in minutes (time.min), no maximum if set to NULL (the default)

Value

Filtered tibble

Examples

fpath <- system.file("extdata", "testfile_flow.isox", package = "isoorbi")
df <-
  orbi_read_isox(file = fpath) |>
  orbi_simplify_isox() |>
  orbi_filter_files(
    filenames = c("s3744"),
    compounds = "HSO4-",
    isotopocules = c("M0", "34S", "18O")
  )
#> ✔ [26ms] 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
#> ✔ [10ms] orbi_filter_isotopocules() removed 860 / 2.15k peaks (40%) because
#> they were not the selected isotopocule M0, 34S, and 18O (860).
#> ✔ [77ms] orbi_filter_files() filtered the dataset by filenames (s3744),
#> compounds (HSO4-), and isotopocules (M0, 34S, 18O) and removed a total of
#> 5.16k/6.45k peaks (80%)