feat: add new filterPeaksRanges function
#326
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- Add a new `filterPeaksRanges` function that allows to filter mass peaks in a `Spectra` by any (combination of) numeric spectra and peaks variables. - Re-organize documentation of filter and subset operations (related to issue #288).
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A nice use case for this function would be to filter a LC-MS data set keeping (or removing) all mass peaks that were considered a chromatographic peak by xcms-based preprocessing. This allows e.g. to evaluate the foreground (i.e. all quantified ion signal) and background signal (i.e. background noise, or signal that was not considered a valid chromatographic peak by xcms) of a full data set. I will later add such a use case to the xcmsTutorials tutorial/workshop. |
R/Spectra-functions.R
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| #' has to be an available spectra or peaks variable. `<range>` can be a | ||
| #' `numeric` of length 2 defining the lower and upper boundary, or a `numeric` | ||
| #' two-column matrix (multi-row matrices are also supported, see further | ||
| #' below). `filterPeaksRanges(s, mz = c(200, 300))` woudl for example reduce |
R/Spectra-functions.R
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| #' the peaks matrices of the `Spectra` object `s` to mass peaks with an m/z | ||
| #' value between 200 and 300. `filterPeaksRanges()` returns the original | ||
| #' `Spectra` object with the filter operation added to the processing queue. | ||
| #' Thus, the filter gets only applied when the peaks data gets extracted |
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maybe "only" in bold to highlight it
R/Spectra-functions.R
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| #' or peaks variables) have to match. | ||
| #' | ||
| #' **Missing value handling**: any comparison which involves a missing value | ||
| #' (beingvit a spectra variable value, a peaks variable value or a value |
R/Spectra-functions.R
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| #' | ||
| #' **Missing value handling**: any comparison which involves a missing value | ||
| #' (beingvit a spectra variable value, a peaks variable value or a value | ||
| #' in one of thevprovided ranges) is treated as a logical `FALSE`. For |
R/Spectra-functions.R
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| #' @note | ||
| #' | ||
| #' In contrast to other *filter* functions, this function does not provide a | ||
| #' `msLevel.` parameter to apply the filter only on spectra of the specified |
R/Spectra-functions.R
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| #' | ||
| #' In contrast to other *filter* functions, this function does not provide a | ||
| #' `msLevel.` parameter to apply the filter only on spectra of the specified | ||
| #' MS levels. In contrast, to apply no, or different, filters to spectra from |
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mmm i'm confused by this sentence
R/Spectra.R
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| #' operations that reduce the number of spectra in the object as well as filters | ||
| #' that reduce the *content* of the `Spectra` object. See section | ||
| #' *Filter peaks data* below for functions that filter the peaks data of a | ||
| #' `Spectra`. |
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maybe to make it extremely clear, we can say the number of spectra in the Spectra object will not change with filters until applyProcessing() is run ?
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I guess here or at the beginning of the filter section
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| ### Filter spectra data | ||
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| These functions comprise subset operations that reduce the total number of |
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Maybe add "directly" or immediately" ?
| ### Filter or aggregate mass peak data | ||
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| These function filter or aggregate the mass peak data (`peaksData()`) of each | ||
| spectrum in a `Spectra` without changing the total number of spectra. |
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as before I would precise "until the applyProcessing() function in run"
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Thanks @philouail ! I addressed all of your points! Hope documentation is now a bit clearer. Happy for additional/extra feedback, otherwise I proceed and merge tomorrow. |
filterPeaksRangesfunction that allows to filter mass peaks in aSpectraby any (combination of) numeric spectra and peaks variables.