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Compute MS1 feature purity for both polarities

MSdev_get_feature_purity.Rd

Per-polarity wrapper around xcms_get_feature_purity. For each available MS1 XcmsExperiment (PositiveMS1 / NegativeMS1), computes the feature-by-sample purity matrix and stores it as assay "purity_matrix" in qdata.

Skips a polarity when purity_matrix already exists unless force = TRUE. Failures are caught per polarity so one missing xcms slot does not abort the other.

Usage

MSdev_get_feature_purity(
  object,
  ppm = 10,
  isolation_half_window = 0.2,
  force = FALSE,
  drop_blank = TRUE,
  ...
)

Arguments

object

MSdev object

ppm

numeric, ppm tolerance for m/z window. Default 10.

isolation_half_window

numeric, half isolation window (m/z). Default 0.2.

force

logical; if FALSE (default), skip a polarity when purity_matrix already exists in qdata. If TRUE, recompute.

drop_blank

logical; retained for API compatibility (unused; blanks are not stripped from qdata).

...

ignored (retained for API compatibility).

Value

MSdev object with updated MS1 xcms qdata assays.

See also

xcms_get_feature_purity