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| *.html |
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [main, master] | ||
| pull_request: | ||
| branches: [main, master] | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
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| name: pkgdown | ||
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| jobs: | ||
| pkgdown: | ||
| runs-on: ubuntu-latest | ||
| # Only restrict concurrency for non-PR jobs | ||
| concurrency: | ||
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| permissions: | ||
| contents: write | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: r-lib/actions/setup-pandoc@v2 | ||
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::pkgdown, local::. | ||
| needs: website | ||
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| - name: Build site | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
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| - name: Deploy to GitHub pages 🚀 | ||
| if: github.event_name != 'pull_request' | ||
| uses: JamesIves/github-pages-deploy-action@v4.4.1 | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
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| #' MS/MS Spectra Extraction from annotated features | ||
| #' | ||
| #' @description This function extracts MS/MS spectra associated with | ||
| #' features annotated by \link[GlycoAnnotateR]{glycoAnnotate} function. | ||
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| #' @param data_ms2 [MSnbase::MSnExp()], [MSnbase::OnDiskMSnExp()] or [xcms::XCMSnExp()] | ||
| #' object with MS/MS spectra. | ||
| #' @param data_features [xcms::XCMSnExp()] with MS1 features defined by XCMS processing | ||
| #' that were annotated by \link[GlycoAnnotateR]{glycoAnnotate}. | ||
| #' @param annotations Output of \link[GlycoAnnotateR]{glycoAnnotate}. It needs to be a | ||
| #' `data.frame` with numerical columns named "mz" and "rt" (mz columns contains *m/z* | ||
| #' of the features, not of the annotations!). | ||
| #' | ||
| #' @return It returns a MSpectra object with all msLevel=2 spectra whose | ||
| #' precursors are the features annotated by \link[GlycoAnnotateR]{glycoAnnotate} function. | ||
| #' | ||
| #' @export | ||
| #' | ||
| #' @seealso [GlycoAnnotateR::glycoPredict()] | ||
| #' @seealso [GlycoAnnotateR::glycoPredictParam()] | ||
| #' | ||
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| glycoMS2Extract = function(data_ms2, data_features, annotations){ | ||
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| # Check if "data_ms2" has msLevel = 2 spectra. | ||
| if(any(table(data_ms2@featureData@data$msLevel, data_ms2@featureData@data$fileIdx)[2,]==0)){ | ||
| stop("Error: Some of the files do not have MS level 2 data.") | ||
| } | ||
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| # Change "data_ms2" into "XCMSnExp" | ||
| data_ms2 = as(data_ms2, "XCMSnExp") | ||
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| # Overwrite "data_ms2" peaks and features for the ones in "data_features" | ||
| chromPeaks(data_ms2) = xcms::chromPeaks(data_features) | ||
| featureDefinition = xcms::featureDefinitions(data_features) | ||
| featureDefinition_filtered = featureDefinition[paste0(featureDefinition$mzmed,"_", featureDefinition$rtmed) %in% | ||
| paste0(annotations$mz,"_",annotations$rt),] | ||
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| featureDefinitions(data_ms2) = featureDefinition_filtered | ||
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| # Get msLevel=2 spectra that is related to defined features. | ||
| MS2Spectra = xcms::featureSpectra(data_ms2, msLevel = 2, expandMz = 0.005) | ||
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| return(MS2Spectra) | ||
| } |
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| url: https://margotbligh.github.io/GlycoAnnotateR/ | ||
| template: | ||
| bootstrap: 5 | ||
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