Hello
I am interested in generating the images from Ralf's Bioinformatics paper in 2008 (Highly sensitive feature detection for high resolution LC/MS). Specifically pages 5,9 and 10 of the m/z domain and the corresponding chromatogram with applied wavelet. If anyone has done this before, I would greatly appreciate a point in the right direction.
Can I extract this data from R as the algorithms are being applied, or will I need a separate software for this generation?
Thank you again-
Ashley Sidebottom
Have you tried using the "sleep" option for centWave which will generate similar visualizations ?
By using something like
pdf(file="myplots.pdf")
xcmsSet(method="centWave", sleep=0.0001,...)
dev.off()
you can save the plots to a pdf file.
To enable the Gaussian fits, turn on "fitgauss=TRUE".
Is there some way to limit what m/z range you get when you do this? I would like to see the Gaussian fit for a particular compound where I know, based on the peakTable, the m/z and RT; how do I do that?