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  "Package": "PCBS",
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  "Title": "Principal Component BiSulfite",
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  "Authors@R": "c(person(\"Kathryn\", \"Lande\", email=\"kathryn.lande@mail.mcgill.ca\", role=c(\"aut\", \"cre\", \"cph\")))",
  "Description": "A system for fast, accurate, and flexible whole genome\nbisulfite sequencing (WGBS) data analysis of two-condition\ncomparisons. Principal Component BiSulfite, 'PCBS', assigns\nmethylated loci eigenvector values from the\ntreatment-delineating principal component in lieu of running\nmillions of pairwise statistical tests, which dramatically\nincreases analysis flexibility and reduces computational\nrequirements. Methods:\n<https://katlande.github.io/PCBS/articles/Differential_Methylation.html>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://github.com/katlande/PCBS",
  "BugReports": "https://github.com/katlande/PCBS/issues",
  "Repository": "https://katlande.r-universe.dev",
  "Date/Publication": "2024-09-04 19:47:05 UTC",
  "RemoteUrl": "https://github.com/katlande/pcbs",
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    "User": "root"
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  "Author": "Kathryn Lande [aut, cre, cph]",
  "Maintainer": "Kathryn Lande <kathryn.lande@mail.mcgill.ca>",
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  "_published": "2026-06-01T10:34:14.214Z",
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  "_assets": [
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      "date": "2024-04-23"
    },
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      "version": "0.1.1",
      "date": "2024-08-27"
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    "CheckOvercompression",
    "checkRank",
    "chromDict",
    "chromDictMeth",
    "DefineBestPC",
    "get_all_DMRs",
    "Get_Novel_DMRs",
    "getPCRanks",
    "getRegionScores",
    "lin",
    "lmIntx",
    "MethyDiff_Set",
    "MethylDiff",
    "methylDiff_metagene",
    "multiple_metagenes",
    "Ol_Reliable",
    "oneSeed",
    "plot_metagene",
    "rankDist",
    "score_metagene",
    "se",
    "tilt",
    "trimDMR"
  ],
  "_datasets": [
    {
      "name": "eigen",
      "title": "Simulated WGBS data for PCBS vignettes",
      "object": "eigen",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cpgID",
        "trt1_PercMeth",
        "trt1_nCpG",
        "trt2_PercMeth",
        "trt2_nCpG",
        "trt3_PercMeth",
        "trt3_nCpG",
        "ctl1_PercMeth",
        "ctl1_nCpG",
        "ctl2_PercMeth",
        "ctl2_nCpG",
        "ctl3_PercMeth",
        "ctl3_nCpG"
      ],
      "rows": 50000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addRanks",
      "title": "Add ranks to eigenvector scores.",
      "topics": [
        "addRanks"
      ]
    },
    {
      "page": "CheckOvercompression",
      "title": "Check if DMR calling seed number is ovcompressed.",
      "topics": [
        "CheckOvercompression"
      ]
    },
    {
      "page": "checkRank",
      "title": "Check rank cut-off values manually.",
      "topics": [
        "checkRank"
      ]
    },
    {
      "page": "chromDict",
      "title": "Convert a rank object into a chromDict.",
      "topics": [
        "chromDict"
      ]
    },
    {
      "page": "chromDictMeth",
      "title": "Create a chromDict of percent methylation difference at all sites.",
      "topics": [
        "chromDictMeth"
      ]
    },
    {
      "page": "DefineBestPC",
      "title": "Identify your best principle component.",
      "topics": [
        "DefineBestPC"
      ]
    },
    {
      "page": "eigen",
      "title": "Simulated WGBS data for PCBS vignettes",
      "topics": [
        "eigen"
      ]
    },
    {
      "page": "get_all_DMRs",
      "title": "Nested DMR calling function within Get_Novel_DMRs()",
      "topics": [
        "get_all_DMRs"
      ]
    },
    {
      "page": "Get_Novel_DMRs",
      "title": "Call DMRs from WGBS data.",
      "topics": [
        "Get_Novel_DMRs"
      ]
    },
    {
      "page": "getPCRanks",
      "title": "Get CpG eigenvector scores from a principle component.",
      "topics": [
        "getPCRanks"
      ]
    },
    {
      "page": "getRegionScores",
      "title": "Calculated methylation significance in a set of regions.",
      "topics": [
        "getRegionScores"
      ]
    },
    {
      "page": "lin",
      "title": "Find y value of linear regression given x.",
      "topics": [
        "lin"
      ]
    },
    {
      "page": "lmIntx",
      "title": "PC-Intersect nested function.",
      "topics": [
        "lmIntx"
      ]
    },
    {
      "page": "MethyDiff_Set",
      "title": "Add a mean methylation column to a data.frame of regions.",
      "topics": [
        "MethyDiff_Set"
      ]
    },
    {
      "page": "MethylDiff",
      "title": "Get the mean methylation difference across a specified region.",
      "topics": [
        "MethylDiff"
      ]
    },
    {
      "page": "methylDiff_metagene",
      "title": "Make a metagene from mean percent methylation differences.",
      "topics": [
        "methylDiff_metagene"
      ]
    },
    {
      "page": "multiple_metagenes",
      "title": "Plot multiple metagene data objects on a single plot.",
      "topics": [
        "multiple_metagenes"
      ]
    },
    {
      "page": "Ol_Reliable",
      "title": "PCBS ggplot theme.",
      "topics": [
        "Ol_Reliable"
      ]
    },
    {
      "page": "oneSeed",
      "title": "Nested DMR calling function within within get_all_DMRs(), Get_Novel_DMRs()",
      "topics": [
        "oneSeed"
      ]
    },
    {
      "page": "plot_metagene",
      "title": "Generate a metagene plot from raw metagene data.",
      "topics": [
        "plot_metagene"
      ]
    },
    {
      "page": "rankDist",
      "title": "Identify the best rank cut-off for significant CpGs.",
      "topics": [
        "rankDist"
      ]
    },
    {
      "page": "score_metagene",
      "title": "Make a metagene from PC Scores.",
      "topics": [
        "score_metagene"
      ]
    },
    {
      "page": "se",
      "title": "Standard error of a vector.",
      "topics": [
        "se"
      ]
    },
    {
      "page": "tilt",
      "title": "Component of PCBS ggplot theme.",
      "topics": [
        "tilt"
      ]
    },
    {
      "page": "trimDMR",
      "title": "Nested DMR calling function within within Get_Novel_DMRs()",
      "topics": [
        "trimDMR"
      ]
    }
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