{
  "_id": "6a1ab0111d7bb097a09d5575",
  "Package": "ramwas",
  "Type": "Package",
  "Title": "Fast Methylome-Wide Association Study Pipeline for Enrichment\nPlatforms",
  "Version": "1.37.0",
  "Date": "2019-02-18",
  "Authors@R": "c(person(\"Andrey A\", \"Shabalin\",\nrole = c(\"aut\", \"cre\"),\nemail = \"andrey.shabalin@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0309-6821\")),\nperson(\"Shaunna L\", \"Clark\",\nemail = \"slclark2@vcu.edu\",\nrole = \"aut\"),\nperson(\"Mohammad W\", \"Hattab\",\nemail = \"mwhattab@vcu.edu\",\nrole = \"aut\"),\nperson(\"Karolina A\", \"Aberg\",\nemail = \"kaaberg@vcu.edu\",\nrole = \"aut\"),\nperson(\"Edwin J C G\", \"van den Oord\",\nemail = \"ejvandenoord@vcu.edu\",\nrole = \"aut\"))",
  "Maintainer": "Andrey A Shabalin <andrey.shabalin@gmail.com>",
  "Description": "A complete toolset for methylome-wide association studies\n(MWAS). It is specifically designed for data from enrichment\nbased methylation assays, but can be applied to other data as\nwell. The analysis pipeline includes seven steps: (1) scanning\naligned reads from BAM files, (2) calculation of quality\ncontrol measures, (3) creation of methylation score (coverage)\nmatrix, (4) principal component analysis for capturing batch\neffects and detection of outliers, (5) association analysis\nwith respect to phenotypes of interest while correcting for top\nPCs and known covariates, (6) annotation of significant\nfindings, and (7) multi-marker analysis (methylation risk\nscore) using elastic net. Additionally, RaMWAS include tools\nfor joint analysis of methlyation and genotype data. This work\nis published in Bioinformatics, Shabalin et al. (2018)\n<doi:10.1093/bioinformatics/bty069>.",
  "URL": "https://bioconductor.org/packages/ramwas/",
  "BugReports": "https://github.com/andreyshabalin/ramwas/issues",
  "License": "LGPL-3",
  "LazyLoad": "yes",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "biocViews": "DNAMethylation, Sequencing, QualityControl, Coverage,\nPreprocessing, Normalization, BatchEffect, PrincipalComponent,\nDifferentialMethylation, Visualization",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:50 UTC",
  "RemoteUrl": "https://github.com/bioc/ramwas",
  "RemoteRef": "HEAD",
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  "Packaged": {
    "Date": "2026-05-30 07:03:45 UTC",
    "User": "root"
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  "Author": "Andrey A Shabalin [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0309-6821>),\nShaunna L Clark [aut],\nMohammad W Hattab [aut],\nKarolina A Aberg [aut],\nEdwin J C G van den Oord [aut]",
  "MD5sum": "3abb0bf89a23cd6febdf85c1d36ddfcb",
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  "_created": "2026-05-30T07:03:45.000Z",
  "_published": "2026-05-30T09:38:24.978Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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  "_homeurl": "https://github.com/andreyshabalin/ramwas",
  "_realowner": "bioc",
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  "_exports": [
    "cachedRDSload",
    "colSumsSq",
    "estimateFragmentSizeDistribution",
    "findBestNpvs",
    "getCpGsetALL",
    "getCpGsetCG",
    "getDataByLocation",
    "getLocations",
    "getMWAS",
    "getMWASandLocations",
    "getMWASrange",
    "injectSNPsMAF",
    "insilicoFASTQ",
    "isAbsolutePath",
    "madeBED",
    "madeBEDgraph",
    "madeBEDgraphRange",
    "madeBEDrange",
    "makefullpath",
    "manPlotFast",
    "manPlotPrepare",
    "mat2cols",
    "orthonormalizeCovariates",
    "parameterDump",
    "parameterPreprocess",
    "parametersFromFile",
    "pipelineProcessBam",
    "plotCVcors",
    "plotFragmentSizeDistributionEstimate",
    "plotPCvalues",
    "plotPCvectors",
    "plotPrediction",
    "plotROC",
    "processCommandLine",
    "pvalue2qvalue",
    "qcmean",
    "qqPlotFast",
    "qqPlotPrepare",
    "ramwas0createArtificialData",
    "ramwas1scanBams",
    "ramwas2collectqc",
    "ramwas3normalizedCoverage",
    "ramwas4PCA",
    "ramwas5MWAS",
    "ramwas6annotateTopFindings",
    "ramwas7ArunMWASes",
    "ramwas7BrunElasticNet",
    "ramwas7CplotByNCpGs",
    "ramwas7riskScoreCV",
    "ramwasAnnotateLocations",
    "ramwasParameters",
    "ramwasSNPs",
    "rowSumsSq",
    "subsetCoverageDirByLocation",
    "testPhenotype"
  ],
  "_help": [
    {
      "page": "RaMWAS",
      "title": "Fast Methylome-wide Association Study Pipeline for Enrichment Platforms",
      "topics": [
        "ramwas-package",
        "ramwas"
      ]
    },
    {
      "page": "cachedRDSload",
      "title": "Cached Loading of RDS Files",
      "topics": [
        "cachedRDSload"
      ]
    },
    {
      "page": "findBestNpvs",
      "title": "Quickly Find N Smallest P-values in a Long Vector",
      "topics": [
        "findBestNpvs"
      ]
    },
    {
      "page": "get",
      "title": "Functions for Access to Data, MWAS Results, and Location Information",
      "topics": [
        "getDataByLocation",
        "getLocations",
        "getMWAS",
        "getMWASandLocations",
        "getMWASrange"
      ]
    },
    {
      "page": "getCpGset",
      "title": "Construct CpG set for a Reference Genome",
      "topics": [
        "getCpGsetALL",
        "getCpGsetCG"
      ]
    },
    {
      "page": "injectSNPsMAF",
      "title": "Inject SNPs from VCF Count File into a DNA Sequence",
      "topics": [
        "injectSNPsMAF"
      ]
    },
    {
      "page": "insilicoFASTQ",
      "title": "Construct FASTQ File for In-silico Alignment Experiment",
      "topics": [
        "insilicoFASTQ"
      ]
    },
    {
      "page": "isAbsolutePath",
      "title": "Check if Path is Absolute.",
      "topics": [
        "isAbsolutePath"
      ]
    },
    {
      "page": "MakeBED",
      "title": "Export MWAS results in BED format.",
      "topics": [
        "madeBED",
        "madeBEDgraph",
        "madeBEDgraphRange",
        "madeBEDrange"
      ]
    },
    {
      "page": "makefullpath",
      "title": "Combine Path and Filename into Filename with Path",
      "topics": [
        "makefullpath"
      ]
    },
    {
      "page": "manhattan",
      "title": "Fast Manhattan plot for Large Number of P-values",
      "topics": [
        "manPlotFast",
        "manPlotPrepare"
      ]
    },
    {
      "page": "mat2cols",
      "title": "Split a Matrix into Column Vectors",
      "topics": [
        "mat2cols"
      ]
    },
    {
      "page": "orthonormalizeCovariates",
      "title": "Orthonormalize Covariates",
      "topics": [
        "orthonormalizeCovariates"
      ]
    },
    {
      "page": "parameterDump",
      "title": "Save Parameters in a Text File",
      "topics": [
        "parameterDump"
      ]
    },
    {
      "page": "parameterPreprocess",
      "title": "Preprocess Pipeline Parameter List.",
      "topics": [
        "parameterPreprocess"
      ]
    },
    {
      "page": "parametersFromFile",
      "title": "Scan Parameters From a R Code File",
      "topics": [
        "parametersFromFile"
      ]
    },
    {
      "page": "pipeline",
      "title": "RaMWAS: High Level Pipeline Functions",
      "topics": [
        "pipeline",
        "pipelineProcessBam",
        "ramwas1scanBams",
        "ramwas2collectqc",
        "ramwas3normalizedCoverage",
        "ramwas4PCA",
        "ramwas5MWAS",
        "ramwas6annotateTopFindings",
        "ramwas7ArunMWASes",
        "ramwas7BrunElasticNet",
        "ramwas7CplotByNCpGs",
        "ramwas7riskScoreCV",
        "ramwasSNPs"
      ]
    },
    {
      "page": "plotCV",
      "title": "Plotting Functions used in Cross Validation Analysis (Methylation Risk Score).",
      "topics": [
        "plotCVcors",
        "plotPrediction",
        "plotROC"
      ]
    },
    {
      "page": "plotFragmentSizeDistributionEstimate",
      "title": "Estimate and plot Fragment Size Distribution.",
      "topics": [
        "estimateFragmentSizeDistribution",
        "plotFragmentSizeDistributionEstimate"
      ]
    },
    {
      "page": "plotPC",
      "title": "Plot Principal component (PC) Values (variation explained) and PC vectors (loadings)",
      "topics": [
        "plotPCvalues",
        "plotPCvectors"
      ]
    },
    {
      "page": "processCommandLine",
      "title": "Scan Parameters From Command Line",
      "topics": [
        "processCommandLine"
      ]
    },
    {
      "page": "pvalue2qvalue",
      "title": "Calculate Benjamini-Hochberg q-values",
      "topics": [
        "pvalue2qvalue"
      ]
    },
    {
      "page": "QCs",
      "title": "Quality Control Measures",
      "topics": [
        "plot.qcCoverageByDensity",
        "plot.qcEditDist",
        "plot.qcEditDistBF",
        "plot.qcHistScore",
        "plot.qcHistScoreBF",
        "plot.qcIsoDist",
        "plot.qcLengthMatched",
        "plot.qcLengthMatchedBF",
        "qcmean",
        "qcmean.NULL",
        "qcmean.qcChrX",
        "qcmean.qcChrY",
        "qcmean.qcCoverageByDensity",
        "qcmean.qcEditDist",
        "qcmean.qcEditDistBF",
        "qcmean.qcFrwrev",
        "qcmean.qcHistScore",
        "qcmean.qcHistScoreBF",
        "qcmean.qcIsoDist",
        "qcmean.qcLengthMatched",
        "qcmean.qcLengthMatchedBF",
        "qcmean.qcNonCpGreads"
      ]
    },
    {
      "page": "qqplotFast",
      "title": "Fast QQ-plot for Large Number of P-values",
      "topics": [
        "qqPlotFast",
        "qqPlotPrepare"
      ]
    },
    {
      "page": "ramwas0createArtificialData",
      "title": "Create Artificial Data Set",
      "topics": [
        "ramwas0createArtificialData"
      ]
    },
    {
      "page": "ramwasAnnotateLocations",
      "title": "Extract Biomart Annotation for a Vector of Locations.",
      "topics": [
        "ramwasAnnotateLocations"
      ]
    },
    {
      "page": "ramwasParameters",
      "title": "Function for Convenient Filling of the RaMWAS Parameter List.",
      "topics": [
        "ramwasParameters"
      ]
    },
    {
      "page": "rowcolSumSq",
      "title": "Form Row and Column Sums of Squares",
      "topics": [
        "colSumsSq",
        "rowSumsSq"
      ]
    },
    {
      "page": "rwDataClass-class",
      "title": "Class for Accessing Data (Coverage) Matrix",
      "topics": [
        "rwDataClass",
        "rwDataClass-class"
      ]
    },
    {
      "page": "subsetData",
      "title": "Subset a data matrix and locations",
      "topics": [
        "subsetCoverageDirByLocation"
      ]
    },
    {
      "page": "testPhenotype",
      "title": "Test the Phenotype of Interest for Association with Methylation Coverage.",
      "topics": [
        "testPhenotype"
      ]
    }
  ],
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      "source": "RW1_intro.Rmd",
      "filename": "RW1_intro.html",
      "title": "RaMWAS Overview",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting started",
        "Installation",
        "Loading package and viewing documentation",
        "RaMWAS steps",
        "Scan BAM files and calculate QC indices",
        "Summarize QC measures",
        "Calculate CpG score matrix",
        "Principal component analysis",
        "Methylome-wide association study (MWAS)",
        "Annotation of top results",
        "Methylation risk score",
        "CpG-SNP analysis",
        "Directory names",
        "Version information",
        "References"
      ],
      "created": "2016-12-12 22:17:22",
      "modified": "2018-08-30 17:54:54",
      "commits": 11
    },
    {
      "source": "RW2_CpG_sets.Rmd",
      "filename": "RW2_CpG_sets.html",
      "title": "CpG sets",
      "engine": "knitr::rmarkdown",
      "headings": [
        "CpG sets",
        "Downloadable CpG sets",
        "Constructing a custom CpG set",
        "Constructing a CpG set for a reference genome",
        "In silico alignment experiment"
      ],
      "created": "2017-04-19 15:31:36",
      "modified": "2018-03-09 17:29:36",
      "commits": 4
    },
    {
      "source": "RW3_BAM_QCs.Rmd",
      "filename": "RW3_BAM_QCs.html",
      "title": "BAM Quality Control Measures",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Loading and saving RaMWAS objects",
        "QC text summary",
        "Quality control measures",
        "The number of BAM files",
        "Total number of reads in the BAM file(s)",
        "Number of reads aligned to the reference genome",
        "Number of reads that passed minimum score filter",
        "Number of reads after removal of duplicate reads",
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