cosmiq (version 1.6.0)

retention_time: Detection of chromatographic peak locations from extracted ion chromatograms (EICs)

Description

For each EIC in the EIC matrix, retention_time localizes chromatographic peaks using peakdetection.

Usage

retention_time(xy, xs, eicmatrix, RTscales, RTSNR.Th, 
RTSNR.area, mintr)

Arguments

xy

table including mz location parameters

xs

xcmsSet object

eicmatrix

Matrix containing extracted ion chromatograms (EICs)

RTscales

Peak Detection of Chromatographic peaks on the combined extracted ion chromatogram: scales for continuous wavelet transformation (CWT), see also the peakDetectionCWT function of the MassSpecWavelet package.

RTSNR.Th

Peak Detection of Chromatographic peaks on the combined extracted ion chromatogram: Signal to noise ratio threshold

RTSNR.area

Peak Detection of Chromatographic peaks on the combined extracted ion chromatogram: Area around the peak for noise determination. Indicates number of surrounding peaks on the first CWT scale. default = 20

mintr

Minimal peak width intensity treshold (in percentage), for which two overlapping peaks are considered as separated (default = 0.5)

Details

Based on the combined extracted ion chromatograms, there is another peak detection step to be performed. The same algorithm as described for the peak picking of mass signals (continuous wavelet transformation) is also used for peak picking in the retention time domain.

Examples

      ## Not run: 
#     #  see package vignette
#       ## End(Not run)