Some updates and bug fixes #761
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- Support coercing from `XcmsExperiment` to `XCMSnExp` using `setAs(object, "XCMSnExp")` (issue #752).
- Change `estimatePrecursorIntensity()` to a method and add an implementation for `MsExperiment`.
- `chromatogram` with `msLevel = 2L` does by default extract chromatographic data of all MS2 spectra, independently of whether different m/z isolation windows were used. For data with isolation windows, the respective isolation window can be set/defined with the `isolationWindowTargetMz` parameter. - Update documentation to describe this behaviour better.
| brew install imagemagick@6 | ||
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| ## For textshaping, required by ragg, and required by pkgdown | ||
| brew install harfbuzz fribidi |
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brew install harfbuzz fribidi seriously ? Somebody was creative there :-) Certainly very google'able...
DESCRIPTION
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| @@ -1,5 +1,5 @@ | |||
| Package: xcms | |||
| Version: 4.3.2 | |||
| Version: 4.3.4 | |||
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Are we skipping 4.3.3 ? I couldn't find a 4.3.3 in a PR.
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True, my mistake. Somehow I forgot to make the 4.3.3 PR. I will revert to 4.3.3 for this PR.
| @@ -54,7 +54,7 @@ Imports: | |||
| methods, | |||
| Biobase, | |||
| BiocGenerics, | |||
| ProtGenerics (>= 1.35.4), | |||
| ProtGenerics (>= 1.37.1), | |||
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That's needed because only the newer has a generic for estimatePrecursorIntensity ?
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Exactly. The estimatePrecursorIntensity generic was added to ProtGenerics version 1.37.1
| @@ -63,7 +63,7 @@ Imports: | |||
| MsCoreUtils (>= 1.15.5), | |||
| MsFeatures, | |||
| MsExperiment (>= 1.5.4), | |||
| Spectra (>= 1.13.7), | |||
| Spectra (>= 1.15.7), | |||
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I Guess needed because only the newer has estimatePrecursorIntensity
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Yes, because for MsExperiment/XcmsExperiment we're using the estimatePrecursorIntensity,Spectra method, while for the older XCMSnExp object we use a different one.
This PR adds:
chromatogram()call withmsLevel = 2L); improve documentation (and vignette) for this.estimatePrecursorIntensity()function to a method and import the generic from ProtGenerics. This ensures we can have different implementations forXcmsExperiment,XCMSnExpand also avoid clashes with the implementation in Spectra forSpectraobjects.XcmsExperimenttoXCMSnExpfor backward compatibility.