Add support for skipFilled in featureSpectra for XcmsExperiment and two bug fixes #815
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- Fix issue #812 : parameters `minFraction` and `maxFeatures` were not correctly considered in `plotChromPeakDensity()`.
- Add parameter `columns` to `chromPeakData()` for `XCMSnExp` and `XcmsExperiment` classes to allow extraction of selected columns.
- Add support for parameter `columns` to the `chromPeakData()` method for `XcmsExperimentHdf5` objects.
- Parameter `skipFilled` is now supported for `featureSpectra,XcmsExperiment`.
- Add unit tests checking that parameter `skipFilled` works correctly for `featureSpectra()` for `XcmsExperimentHdf5` objects.
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@sneumann , sorry to be a bit pushy here, but we should try to manage getting this PR into xcms before the next Bioconductor release. This contains some important bug fixes. |
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In this PR:
XcmsExperimentobjects toXCMSnExp(issue Convert XcmsExperiment to XCMSnExp object error #807).columnstochromPeakData()to allow extraction of selected columns.skipFilledtofeatureSpectra()forXcmsExperimentandXcmsExperimentHdf5to avoid extraction of spectra for gap-filled chromatographic peaks.spectraData()method from Spectra.