Build xcms centWave roiList from mz/rt targets — get_xcms_roi

Construct a roiList accepted by xcms::CentWaveParam(roiList = ...). Input a matrix/data.frame with columns mz and rt (seconds). For each target, mzmin/mzmax are calculated using ppm tolerance and the RT window rtmin/rtmax is mapped to scan indices.

Scan indices are computed per file from MS1 spectra, then expanded to the union range across files and clamped to [1, min(n_MS1)] so one shared roiList stays valid for every file in findChromPeaks(). Unclamped unions can overflow shorter runs and raise Error in scanrange inside .centWave_orig.

Note: scmin/scmax must be finite integer scan indices (not c(0, Inf)). centWave uses them in arithmetic (N <- scmax - scmin + 1) before clipping to each file's length(scantime).

Usage

get_xcms_roi_list(mzrt, xcms.xcms, ppm = 10, rt_tol = 30, ion_mode = NULL)

Arguments

mzrt: matrix/data.frame with columns mz and rt.
xcms.xcms: XCMSnExp, MsExperiment, or XcmsExperiment used to map RT to scan indices.
ppm: numeric, ppm tolerance for mz window.
rt_tol: numeric, RT tolerance in seconds.
ion_mode: optional integer 1 (positive) or 0 (negative). If NULL, inferred from scan polarity; must be unique.

Value

list of ROI objects (each ROI is a list with scmin, scmax, mzmin, mzmax, length, intensity).