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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Expanding peakrange in fillpeaks #2

Closed stanstrup closed 6 years ago

stanstrup commented 10 years ago

Hi. I don't know if this is now the proper place to post suggestions but here it goes.

As have been noted previously (http://metabolomics-forum.com/viewtopic.php?f=25&t=148) the peak range for the initially picked peaks can be too narrow to allow proper re-integration for all samples.

I suggest that a parameter to expand peakrange in getPeaks is added to fillPeaks.chrom and passed on to fillPeaksChromPar. I don't know the what the most appropriate way to pass the parameter would be so hence no pull request.

I suggest the multiplier is used like this: you set M=0.1 if you want to increase the peakrange interval by 10%

the peakrange to use in getPeaks then becomes:

mzmax_new = mzmax + ((mzmax-mzmin)_M)/2 mzmin_new = mzmin - ((mzmax-mzmin)_M)/2

stanstrup commented 8 years ago

I have reopened this. See the pull request here: https://github.com/sneumann/xcms/pull/3 What needs to happen to get this included?

stanstrup commented 8 years ago

Forgot to say that I would really like this included as soon as possible since the version the pull request was based on is no longer compatible with current versions of the dependencies, so I cannot use my fork.

stanstrup commented 7 years ago

Is it possible to use FillChromPeaksParam (so that you can use the ppm setting that sets a minimum width) in the old workflow? I still consider this a pretty critical issue that current fillpeaks will try to integrate in an essentially 0 width m/z slice.

jorainer commented 7 years ago

Unfortunately FillChromPeaksParam can not be used in the old workflow. The new fillChromPeaks uses completely different code, i.e. it really reads raw data to fill in peaks. In the old workflow, even if you used centWave and thus did never have the need for the profile matrix, the peaks are filled in from the profile matrix.

I'll check if and how I can include this parameter in the old workflow too.

stanstrup commented 7 years ago

Thanks. I did make a pull request for a minimum widths of mz and rt. Just used absolute widths instead of ppm. I think you also found a bug in my code though. Right now there are only the expand options while the minimum options would be more helpful.

jorainer commented 6 years ago

Closing this issue (the oldest one we've had still open!), because this feature is added in the new user interface functions: possibility to expand the are by a constant or relative value in both m/z and rt dimension.