Compute MS1 purity matrix for xcms features — get_xcms_feature_purity

Calculate a feature-by-sample MS1 purity matrix by extracting, for each feature in xcms.xcms, the closest MS1 scan (by retention time) from xcms.ms1.sp in each sample file (matched by Spectra::dataOrigin). Purity is calculated within an isolation window around the feature m/z.

If xcms.ms1.sp is not provided, MS1 spectra are taken via ProtGenerics::spectra(xcms.xcms) and filtered to MS level 1.

Optimized path: closest-scan lookup via findInterval, a single peaksData() extraction, and purity computed on peak matrices (no per-feature Spectra subsetting).

Usage

get_xcms_feature_purity_matrix(
  xcms.xcms,
  xcms.ms1.sp = NULL,
  ppm = 5,
  isolation_half_window = 0.2
)

Arguments

xcms.xcms: XCMSnExp with grouped features (must have featureDefinitions).
xcms.ms1.sp: Optional MS1 Spectra covering the same files as xcms.xcms. If missing or NULL, taken from ProtGenerics::spectra().
ppm: numeric, ppm tolerance for m/z window.
isolation_half_window: numeric, half isolation window (m/z).

Value

numeric matrix with rows = feature_id, columns = sample files (by dataOrigin).