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XCMS / How to export Xset object intensity data?
I am working on my master thesis on comparing metabolomics MS pipelines, batch effect removal and parameter optimization of the pipeline. And wanted to check that I am doing what I think I am doing.
I wish to convert my xset object into a matrix I(peak groups, sample) where each cell represents the intensity for that peak group in that sample and then I will store the meta-data separately. I have gotten it to work by extracting the xset@peaks, xset@groupidx and xset@groups. Then i fetch the intensities by a for loop:
for each groupidx gidx
for each peak in peaks(gidx)
I(gidx, peak.sample) = I(gidx, peak.sample) + peaks.intf
So my questions are:
- is there an easier/more elegant way to do this?(e.g. some internal function/property in Xcms I missed?)
- is the intensities fetched by fillPeaks() included in peaks & groupidx or will my algorithm miss this data?
- is intf the "standard" measure of intensity of a peak or is one of the other(maxf or even maxo, into) more commonly used?
(Sidenote: I searched for some benchmark datasets to include in my analysis (I have access to an inhouse dataset, but ideally using an established benchmark is better). I found the 'centWave' dataset and the 'IPO-package' datasets, is there any other?)