From xcmsRaw to xcmsSet

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From xcmsRaw to xcmsSet

October 24, 2016, 01:45:24 PM

If I have a list of xcmsRaw object, could I use them to construct xcmsSet by a function such as `getXcmsSet`? Input is a list of xcmsRaw and the group information.

Or could I directly operate the raw data matrix in a xcmsSet to subset data by some rules?

Thanks,

yufree

Re: From xcmsRaw to xcmsSet

Reply #1 – October 24, 2016, 02:19:37 PM

The normal pipeline is to use xcmsSet that just takes file paths as input.
An xcmsSet can be subsetted using split and merged with c. Peak grouping info will be lost.
You'd normally use findPeaks to get peaks from a single xcmsRaw object but there seem to be no way to go from xcmsPeaks (output of findPeaks) to xcmsSet object. At least that I know of. It could probably be extracted from the source code of xcmsSet though.

Re: From xcmsRaw to xcmsSet

Reply #2 – October 24, 2016, 08:05:29 PM

Thanks!

findpeaks is enough for me. I am reading the source code to see if I could rebuild one. I found findPeaksPar which connect the xcmsset with xcmsraw.

ps: I could understand using parallel computation is good. However, the default setting just don't work until I changed BPPARAM into SnowParam() on my Macbook.