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Topics - cpataki

1
XCMS / peak group detected with `peakDensityParam` but not listed in feature matrix
I used the code below on my data, and I detect the following peak group (see screenshot of peaks). However, when I export the feature details, this feature group is not listed (see screenshot of filtered feature definitions). The closest feature group detected is well outside of the retention time window of the peaks plotted. Any help or explanation would be greatly appreciated.

rtr_1 <- c(155, 175)
mzr <- c(153.05351119538767, 153.05504173815234)
gparam <- PeakDensityParam(sampleGroups=fgroups,
                            minFraction = 1/nrow(filegroups),
                            bw = 3,
                            binSize = .025,
                            maxFeatures = 100)
chr <- chromatogram(xset5, rt = rtr_1 , mz = mzr)
plot(chr)#, col = paste0(cols, 80))
highlightChromPeaks(xset5, rt = rtr_1, mz = mzr)
par(mar = c(4.5, 4.5, 1, 0))
plotChromPeakDensity(xset5, mz = mzr, param = gparam, xlim = rtr_1)



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