Check and fix scanrange sub-setting in findPeaks methods

[jorainer]

If scanrange argument is defined, the feature detection should only be performed in the specified scan range. This does not seem to be the case for all findPeaks.* methods!

[jorainer]

A [ method to subset xcmsRaw objects to specific scans/spectra has been added in commit f82432a . This can be used (instead of the split method) to subset the xcmsRaw object(s) prior to feature detection.

[jorainer]

findPeaks.matchedFilter does actually not subset on scanrange: see #63.

[jorainer]

There is also a problem with findPeaks.centWave, see #64

[sneumann]

It would be good to fix this for all the findPeaks.* methods.
What about fillPeaks() ? Since fillPeaks() uses information in seconds,
this should be fine. What about the getEIC() ? Likewise, they use seconds.
Would it make sense to deprecate the scanrange and replace by rtrange=...' to be consistent with other functions likeplotRaw()` ? Yours, Steffen

[jorainer]

Haven't looked specifically at fillPeaks yet, but there shouldn't be any problem there. As mentioned further above, I suggest to use the new [ subsetting method on the xcmsRaw object at the beginning of each method, if !missing(scanrange).
Regarding rtrange and/or scanrange: for now I would like to keep both, also because in MSnbase there is no sub-setting on rtrange implemented (yet).

[jorainer]

Closing: xcmsRaw objects are now sub-setted prior to feature detection for all findPeaks methods.