Store MS1 feature purity matrix in XcmsExperiment qdata

Compute a feature-by-sample MS1 purity matrix and store it as assay "purity_matrix" in MsExperiment::qdata(xcms.xcms).

Requires an XcmsExperiment. MS1 spectra are taken from ProtGenerics::spectra(xcms.xcms) filtered with Spectra::filterMsLevel(1L). The matrix is computed by get_xcms_feature_purity_matrix. If qdata is missing, it is created with xcms::quantify() (assay "raw"), then assay "purity_matrix" is added. Does not write aggregated purity into featureDefinitions.

Usage

xcms_get_feature_purity(xcms.xcms, ppm = 10, isolation_half_window = 0.2)

Arguments

xcms.xcms

XcmsExperiment with grouped features.

ppm

numeric, ppm tolerance for m/z window.

isolation_half_window

numeric, half isolation window (m/z).

Value

XcmsExperiment with qdata containing assay "purity_matrix" (aligned to existing qdata rows/columns).

See also

get_xcms_feature_purity_matrix