retention_time: Detection of chromatographic peak locations from extracted...

In dajofischer/cosmiq: cosmiq - COmbining Single Masses Into Quantities

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.

Author(s)

David Fischer 2013

Examples

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

dajofischer/cosmiq documentation built on June 3, 2019, 6:21 p.m.