Hi,
when I run findPeaks.centWave for a single sample I have
sample@xcmsSet@peaks[1,]
mz mzmin mzmax rt rtmin rtmax into intb
883.9883 883.9843 883.9926 3.4120 2.0610 4.7630 788.7590 786.0570
maxo sn egauss mu sigma h f dppm
321.0089 320.0000 NA NA NA NA 136.0000 9.0000
scale scpos scmin scmax lmin lmax sample
4.0000 3.0000 1.0000 7.0000 1.0000 5.0000 1.0000
and I can access the signal to noise ratio (sn), but for multiple samples it is not present
psample@xcmsSet@peaks[1,]
mz mzmin mzmax rt rtmin rtmax
83.057046 83.057007 83.057068 1.829970 0.333661 6.427780
into maxo sample
22459.443811 4354.406250 1.000000
is there an average or a combined value that I can export?
thks
Using the grouping information (indices) from the group'ed xcmsSet, you can simply pull out all the values you need from the full peak matrix and calculate the S/N statistics for each feature as needed.