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Filter isofiles by mass

Source: R/metadata.R
ir_filter_masses.Rd

Keeps only the requested masses in the traces, cycles, and scans data of either an ir_aggregate_isofiles() result (ir_aggregated_data) or a collection of isofiles read with ir_read_isofiles() (ir_isofiles). Like ir_filter_metadata() it works on both object types and returns the same type it was given.

Usage

ir_filter_masses(isofiles, mass)

Arguments

isofiles

datasets aggregated from ir_aggregate_isofiles() (ir_aggregated_data) or a collection of isofiles from ir_read_isofiles() (ir_isofiles)

mass

which masses to keep, as a tidyselect expression evaluated as if the masses present in the data were column names

  • the same syntax as the mass argument of ir_plot_traces(). E.g. c("44", "45") or 44:48 for specific masses, -"45"/!"45" to exclude one, everything() for all of them, and helpers such as starts_with("4"), matches(), all_of(), or any_of(). Unlike plain tidyselect, numbers select by name rather than by position (44:48 means the masses 44 to 48, not the 44th to 48th mass). Selecting a mass that is not in the data is an error that lists the available masses; use any_of() to ignore missing ones.

Value

the isofiles object (of the same type as the input) with only the selected masses

Details

Any metadata record (uidx + analysis) that has no data left in any of traces/cycles/scans afterwards is removed from the metadata, and the removal cascades to the other datasets exactly as in ir_filter_metadata() (resistors and problems are restricted to the remaining uidx). For an ir_isofiles object, a file whose metadata ends up empty is dropped from the collection entirely. Note that this also drops records that never had any traces/cycles/scans data to begin with (e.g. a file that failed to read) - check ir_get_problems() before filtering if you need to keep track of those.

The mass selection is always resolved once against the whole object (all files of an ir_isofiles collection, and all of traces/cycles/scans of an aggregated dataset combined), so selecting a mass that only some of the files or datasets contain works and simply leaves the others without data.

Ratios calculated with ir_calculate_ratios() live in the ratio_name / ratio columns of the rows of their numerator mass, so they are kept or removed with that mass: filtering to mass = 44 also removes the "45/44" ratio (which sits on the mass 45 rows), while mass = c(44, 45) keeps it. resistors are never filtered by mass since they describe the instrument configuration rather than measured data.

As for the metadata operations, columns that are entirely NA across all remaining rows are dropped from every (non-empty) dataset and the not-aggregated column information is cleared.

Examples

if (FALSE) { # \dontrun{
# keep only the CO2 masses
dataset |> ir_filter_masses(44:46)

# keep everything except mass 45
dataset |> ir_filter_masses(-"45")
} # }