feat: add support for Chromatograms to chromatogram - #837
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- `chromatogram,XcmsExperiment` and `chromatogram,MsExperiment` now allow to return the results as a `Chromatograms` object.
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@philouail , can you please have a look. I will work also on the |
philouail
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looks completely fine to me, just that one comment. thanks
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| #' @param dataOrigin `character` with the **unique** file names/data origin. | ||
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| #' @param isolationWindowTargetMz optional `numeric` of length equal to the |
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maybe add @PARAM msLevel precising that it will be rep() to the length of the object
- `chromPeakChromatograms()` can also return the EICs as a `Chromatograms` object.
- `featureChromatograms()` can now also return the results as a `Chromatograms` object.
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OK, @philouail , now it's ready for review. |
- Add support for `Chromatograms` to the `XcmsExperimentHdf5` result object. - Add new methods `featureChromPeaks()` and `featurePeakidx()` to access the mapping between features and chromatographic peaks.
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Note: |
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@sneumann , this PR is ready for review - and merge. it adds support for the new |
- Fix for issue #839: `chromPeakData<-` for `XcmsExperiment` supports `data.frame` and `DataFrame` as input.
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Includes now also the fix for #839 |
- Import `group()` from BiocGenerics to avoid overriding.
| features = character(), | ||
| mzmin = min, mzmax = max, | ||
| rtmin = min, rtmax = max, | ||
| chunkSize = 2L, ..., |
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I didn't know you can mix ... into the middle of named parameters.
| MetaboCoreUtils (>= 1.11.2), | ||
| data.table | ||
| data.table, | ||
| Chromatograms (>= 1.3.3) |
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BioC devel currently has Chromatograms 1.3.2, but the PR works if installed from GH.
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chromatogram,XcmsExperimentandchromatogram,MsExperimentnow allow to return the results as aChromatogramsobject.