{
  "name": "XCMS processing stages and result inspection",
  "description": "Original crosswalk combining the official release walkthrough with XCMS function references. It connects each processing operation to its documented configuration and the result accessor used for inspection; it contains no measured experimental results.",
  "page": "https://casrai.org/guides/xcms",
  "publisher": "CASRAI",
  "license": "https://creativecommons.org/licenses/by/4.0/",
  "dateModified": "2026-11-14T17:03:19Z",
  "temporalCoverage": null,
  "spatialCoverage": null,
  "columns": [
    {
      "name": "Stage",
      "unit": "",
      "description": ""
    },
    {
      "name": "Processing function",
      "unit": "",
      "description": ""
    },
    {
      "name": "Configuration",
      "unit": "",
      "description": ""
    },
    {
      "name": "Result inspection",
      "unit": "",
      "description": ""
    },
    {
      "name": "Source",
      "unit": "",
      "description": ""
    }
  ],
  "rows": [
    {
      "Stage": "Peak detection",
      "Processing function": "findChromPeaks",
      "Configuration": "CentWaveParam",
      "Result inspection": "chromPeaks: individual peaks within samples",
      "Source": "https://sneumann.github.io/xcms/reference/findChromPeaks.html"
    },
    {
      "Stage": "Retention-time alignment",
      "Processing function": "adjustRtime",
      "Configuration": "ObiwarpParam in the release example",
      "Result inspection": "adjustedRtime: corrected retention-time coordinates",
      "Source": "https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html"
    },
    {
      "Stage": "Correspondence",
      "Processing function": "groupChromPeaks",
      "Configuration": "PeakDensityParam: sampleGroups and minFraction",
      "Result inspection": "featureDefinitions: peaks grouped into features",
      "Source": "https://sneumann.github.io/xcms/reference/groupChromPeaks.html"
    },
    {
      "Stage": "Gap filling",
      "Processing function": "fillChromPeaks",
      "Configuration": "ChromPeakAreaParam",
      "Result inspection": "chromPeakData: is_filled identifies filled peak records",
      "Source": "https://sneumann.github.io/xcms/reference/fillChromPeaks.html"
    },
    {
      "Stage": "Abundance extraction",
      "Processing function": "featureValues",
      "Configuration": "value selects the measurement; method resolves multiple peaks",
      "Result inspection": "Matrix with feature rows and sample columns",
      "Source": "https://sneumann.github.io/xcms/reference/XcmsExperiment.html"
    }
  ],
  "sources": [
    {
      "title": "XCMS release walkthrough",
      "url": "https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html",
      "accessed": "2026-11-14"
    },
    {
      "title": "Chromatographic peak detection",
      "url": "https://sneumann.github.io/xcms/reference/findChromPeaks.html",
      "accessed": "2026-11-14"
    },
    {
      "title": "Correspondence and sample-group criteria",
      "url": "https://sneumann.github.io/xcms/reference/groupChromPeaks.html",
      "accessed": "2026-11-14"
    },
    {
      "title": "Gap filling",
      "url": "https://sneumann.github.io/xcms/reference/fillChromPeaks.html",
      "accessed": "2026-11-14"
    },
    {
      "title": "Result objects and matrix extraction",
      "url": "https://sneumann.github.io/xcms/reference/XcmsExperiment.html",
      "accessed": "2026-11-14"
    }
  ]
}