Xcms feature se.
Extracts and adds median retention time, signal-to-noise ratio, and maximum intensity for each feature. While xcms::featureDefinitions() provides median mz and rt, this function calculates median values across all peaks within a feature: peakRtMin, peakRtMax, peakWidth, peakMzMin, peakMzMax, peakSN, peakMaxo, and polarity.
Convert xcms features to SummarizedExperiment and compute feature-level statistics.
Usage
get_xcms_feature_se(xcms.xcms, ...)
xcms_get_feature_def_stat(xcms.xcms)
Arguments
- xcms.xcms
XCMSnExp object with feature definitions and chromPeaks.
- missing
how missing values should be reported. Allowed values are NA (the default), a numeric or missing = "rowmin_half". The latter replaces any NA with half of the row's minimal (non-missing) value.
Value
SummarizedExperiment
XCMSnExp object with updated featureDefinitions containing additional statistics.
Functions
get_xcms_feature_se(): extract feature data from xcms, convert to SummarizedExperiment
xcms_get_feature_def_stat(): calculate feature statistics