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 toNULL
(the default)- time_max
Maximum retention time in minutes (
time.min
), no maximum if set toNULL
(the default)
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")
)
#> ✔ [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
#> ✔ [10ms] orbi_filter_isotopocules() removed 860 / 2.15k peaks (40%) because
#> they were not the selected isotopocule M0, 34S, and 18O (860).
#> ✔ [76ms] 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%)