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  "Package": "bapred",
  "Type": "Package",
  "Title": "Batch Effect Removal and Addon Normalization (in Phenotype\nPrediction using Gene Data)",
  "Version": "1.1",
  "Date": "2022-06-21",
  "Author": "Roman Hornung, David Causeur",
  "Maintainer": "Roman Hornung <hornung@ibe.med.uni-muenchen.de>",
  "Description": "Various tools dealing with batch effects, in particular\nenabling the removal of discrepancies between training and test\nsets in prediction scenarios. Moreover, addon quantile\nnormalization and addon RMA normalization (Kostka & Spang,\n2008) is implemented to enable integrating the quantile\nnormalization step into prediction rules. The following batch\neffect removal methods are implemented: FAbatch, ComBat,\n(f)SVA, mean-centering, standardization, Ratio-A and Ratio-G.\nFor each of these we provide an additional function which\nenables a posteriori ('addon') batch effect removal in\nindependent batches ('test data'). Here, the (already batch\neffect adjusted) training data is not altered. For evaluating\nthe success of batch effect adjustment several metrics are\nprovided. Moreover, the package implements a plot for the\nvisualization of batch effects using principal component\nanalysis. The main functions of the package for batch effect\nadjustment are ba() and baaddon() which enable batch effect\nremoval and addon batch effect removal, respectively, with one\nof the seven methods mentioned above. Another important\nfunction here is bametric() which is a wrapper function for all\nimplemented methods for evaluating the success of batch effect\nremoval. For (addon) quantile normalization and (addon) RMA\nnormalization the functions qunormtrain(), qunormaddon(),\nrmatrain() and rmaaddon() can be used.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Repository": "https://romanhornung.r-universe.dev",
  "Date/Publication": "2022-06-22 07:20:13 UTC",
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    "author": "Roman Hornung <hornung@ibe.med.uni-muenchen.de>",
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    "kldistTwo",
    "list.batch",
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    "mypvcaBatchAssess",
    "nbfactors",
    "noba",
    "nobaaddon",
    "normalizeAffyBatchqntval",
    "normalizeqntadd",
    "normalizeqntadd2",
    "normalizeqntval",
    "pcplot",
    "plotcomp",
    "postmean",
    "postvar",
    "pvcam",
    "qunormaddon",
    "qunormtrain",
    "ratioa",
    "ratioaaddon",
    "ratiog",
    "ratiogaddon",
    "rmaaddon",
    "rmatrain",
    "sepscore",
    "sepscoreTwo",
    "skewdiv",
    "skewdivTwo",
    "standardize",
    "standardizeaddon",
    "summarizeadd2",
    "summarizeval2",
    "svaba",
    "svabaaddon",
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      "file": "autism.rda",
      "class": [
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        "array"
      ],
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      "table": true,
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      "title": "The bapred package",
      "topics": [
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        "bapred"
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      "topics": [
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    },
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    },
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