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Group xcms Features

xcms_extension_feature_group.Rd

Groups features from an XCMSnExp object using multiple criteria: similarity in retention time, abundance (intensity) correlation, and EIC (extracted ion chromatogram) correlation. RT/abundance grouping uses MsFeatures; EIC similarity uses xcms::EicSimilarityParam.

Group xcms features by retention time, abundance correlation, and EIC similarity.

Usage

xcms_get_feature_group(xcms.xcms, diffRt = 5, intCor = 0.5, eicCor = 0.5)

Arguments

xcms.xcms

XCMSnExp object containing feature definitions.

diffRt

numeric. Maximum allowed retention time difference for grouping by SimilarRtimeParam. If NULL, retention time grouping is skipped. Default is 5.

intCor

numeric. Threshold for abundance similarity (correlation) grouping using AbundanceSimilarityParam. If NULL, intensity correlation grouping is skipped. Default is 0.5.

eicCor

numeric. Threshold for EIC similarity grouping using xcms::EicSimilarityParam. If NULL, EIC correlation grouping is skipped. Default is 0.5.

Value

XCMSnExp object with featureGroups column added or updated.

Functions

  • xcms_get_feature_group(): group features