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  "_rbuild": "4.6.2",
  "_assets": [
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    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.html",
    "extra/NEWS.txt",
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    "extra/VariantFiltering.html"
  ],
  "_homeurl": "https://github.com/rcastelo/variantfiltering",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aaChangeType",
    "aaChangeType<-",
    "allVariants",
    "annoGroups",
    "autosomalDominant",
    "autosomalRecessiveHeterozygous",
    "autosomalRecessiveHomozygous",
    "bamFiles",
    "bamFiles<-",
    "browseVariants",
    "change<-",
    "conservedPositions",
    "cutoffs",
    "cutoffs<-",
    "dbSNPpresent",
    "dbSNPpresent<-",
    "deNovo",
    "downstream",
    "downstream<-",
    "filteredVariants",
    "filters",
    "filters<-",
    "filtersMetadata",
    "FiveSpliceSiteVariants",
    "genePhylostrata",
    "GenePhylostrataDb",
    "genePhylostratum",
    "humanGenesPhylostrata",
    "inheritanceModel",
    "MAFpop",
    "MAFpop<-",
    "maxMAF",
    "maxMAF<-",
    "minCUFC",
    "minCUFC<-",
    "minIntronLength",
    "minIntronLength<-",
    "minPhastCons",
    "minPhastCons<-",
    "minPhylostratum",
    "minPhylostratum<-",
    "minScore3ss",
    "minScore3ss<-",
    "minScore5ss",
    "minScore5ss<-",
    "naMAF",
    "naMAF<-",
    "OMIMpresent",
    "OMIMpresent<-",
    "param",
    "readAAradicalChangeMatrix",
    "readWm",
    "reportVariants",
    "resetSamples",
    "samples",
    "samples<-",
    "sequence_variant.gSOXP",
    "show",
    "softFilterMatrix",
    "softFilterMatrix<-",
    "sog",
    "sortings",
    "sortings<-",
    "spliceSiteMatricesHuman",
    "summary",
    "ThreeSpliceSiteVariants",
    "unrelatedIndividuals",
    "upstream",
    "upstream<-",
    "variantConsequence",
    "variantConsequence<-",
    "VariantFilteringParam",
    "variantLocation",
    "variantLocation<-",
    "variantLocations",
    "variantType",
    "variantType<-",
    "width",
    "wmFilename",
    "wmLocations",
    "wmLocations<-",
    "wmName",
    "wmScore",
    "wmStrictLocations",
    "wmStrictLocations<-",
    "xLinked"
  ],
  "_help": [
    {
      "page": "VariantFiltering-package",
      "title": "Filtering of coding and non-coding genetic variants",
      "topics": [
        "VariantFiltering-package",
        "VariantFiltering"
      ]
    },
    {
      "page": "autosomalDominant",
      "title": "Autosomal dominant inheritance analysis",
      "topics": [
        "autosomalDominant",
        "autosomalDominant,VariantFilteringParam-method"
      ]
    },
    {
      "page": "autosomalRecessiveHeterozygous",
      "title": "Autosomal recessive inheritance analysis: Heterozygous",
      "topics": [
        "autosomalRecessiveHeterozygous",
        "autosomalRecessiveHeterozygous,VariantFilteringParam-method"
      ]
    },
    {
      "page": "autosomalRecessiveHomozygous",
      "title": "Autosomal recessive inheritance analysis: Homozygous",
      "topics": [
        "autosomalRecessiveHomozygous",
        "autosomalRecessiveHomozygous,VariantFilteringParam-method"
      ]
    },
    {
      "page": "deNovo",
      "title": "De Novo variants analysis",
      "topics": [
        "deNovo",
        "deNovo,VariantFilteringParam-method"
      ]
    },
    {
      "page": "GenePhylostrataDb-class",
      "title": "PhastConsDb class",
      "topics": [
        "genePhylostrata",
        "genePhylostrata,GenePhylostrataDb-method",
        "GenePhylostrataDb",
        "GenePhylostrataDb-class",
        "genePhylostratum",
        "genePhylostratum,GenePhylostrataDb,character-method",
        "genePhylostratum,GenePhylostrataDb,missing-method",
        "genePhylostratum,GenePhylostrataDb-method",
        "humanGenesPhylostrata",
        "organism,GenePhylostrataDb-method",
        "show,GenePhylostrataDb-method"
      ]
    },
    {
      "page": "readAAradicalChangeMatrix",
      "title": "Read matrix of amino acid radical changes",
      "topics": [
        "readAAradicalChangeMatrix"
      ]
    },
    {
      "page": "unrelatedIndividuals",
      "title": "Analysis designed to be applied over a group of unrelated individuals",
      "topics": [
        "unrelatedIndividuals",
        "unrelatedIndividuals,VariantFilteringParam-method"
      ]
    },
    {
      "page": "VariantFilteringParam-class",
      "title": "VariantFiltering parameter class",
      "topics": [
        "$,VariantFilteringParam-method",
        "class:VariantFilteringParam",
        "cutoffs,VariantFilteringParam-method",
        "filters,VariantFilteringParam-method",
        "names,VariantFilteringParam-method",
        "sequence_variant.gSOXP",
        "show,VariantFilteringParam-method",
        "sog,VariantFilteringParam-method",
        "spliceSiteMatricesHuman",
        "VariantFilteringParam",
        "VariantFilteringParam-class",
        "variantLocations"
      ]
    },
    {
      "page": "VariantFilteringResults-class",
      "title": "VariantFilteringResults class",
      "topics": [
        "allVariants",
        "allVariants,VariantFilteringResults-method",
        "annoGroups",
        "annoGroups,VariantFilteringResults-method",
        "bamFiles",
        "bamFiles,VariantFilteringResults-method",
        "bamFiles<-",
        "bamFiles<-,VariantFilteringResults,BamViews-method",
        "bamFiles<-,VariantFilteringResults-method",
        "browseVariants",
        "change",
        "change<-",
        "change<-,CutoffsList",
        "change<-,CutoffsList,ANY,character-method",
        "change<-,CutoffsList,ANY,integer-method",
        "change<-,CutoffsList,ANY,logical-method",
        "change<-,CutoffsList,ANY,numeric-method",
        "class:CutoffsList",
        "class:VariantFilteringResults",
        "cutoffs",
        "cutoffs,VariantFilteringResults-method",
        "cutoffs<-",
        "cutoffs<-,VariantFilteringResults,CutoffsList-method",
        "cutoffs<-,VariantFilteringResults,logical-method",
        "cutoffs<-,VariantFilteringResults-method",
        "CutoffsList",
        "CutoffsList-class",
        "filteredVariants",
        "filteredVariants,VariantFilteringResults-method",
        "filters",
        "filters,VariantFilteringResults-method",
        "filters<-",
        "filters<-,VariantFilteringResults-method",
        "filtersMetadata",
        "filtersMetadata,VariantFilteringParam-method",
        "filtersMetadata,VariantFilteringResults-method",
        "inheritanceModel",
        "inheritanceModel,VariantFilteringResults-method",
        "length",
        "length,VariantFilteringResults-method",
        "param",
        "param,VariantFilteringResults-method",
        "plot,VariantFilteringResults,ANY-method",
        "referenceGenome,VariantFilteringResults-method",
        "reportVariants",
        "reportVariants,VariantFilteringResults-method",
        "resetSamples",
        "resetSamples,VariantFilteringResults-method",
        "samples",
        "samples,VariantFilteringResults-method",
        "samples<-",
        "samples<-,VariantFilteringResults,character-method",
        "samples<-,VariantFilteringResults-method",
        "show,CompressedVRangesList-method",
        "show,VariantFilteringResults-method",
        "show,VariantFilteringResultsUI-method",
        "softFilterMatrix,VariantFilteringResults-method",
        "softFilterMatrix<-,VariantFilteringResults-method",
        "sog",
        "sog,VariantFilteringResults-method",
        "sortings",
        "sortings,VariantFilteringResults-method",
        "sortings<-",
        "sortings<-,VariantFilteringResults,CutoffsList-method",
        "summary,VariantFilteringResults-method",
        "VariantFilteringResults",
        "VariantFilteringResults-class"
      ]
    },
    {
      "page": "VariantType-class",
      "title": "FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType",
      "topics": [
        "downstream",
        "downstream,FiveSpliceSiteVariants-method",
        "downstream,ThreeSpliceSiteVariants-method",
        "downstream<-",
        "downstream<-,FiveSpliceSiteVariants-method",
        "downstream<-,ThreeSpliceSiteVariants-method",
        "FiveSpliceSiteVariants",
        "FiveSpliceSiteVariants-class",
        "minIntronLength",
        "minIntronLength,FiveSpliceSiteVariants-method",
        "minIntronLength,ThreeSpliceSiteVariants-method",
        "minIntronLength<-",
        "minIntronLength<-,FiveSpliceSiteVariants-method",
        "minIntronLength<-,ThreeSpliceSiteVariants-method",
        "show,FiveSpliceSiteVariants-method",
        "show,ThreeSpliceSiteVariants-method",
        "ThreeSpliceSiteVariants",
        "ThreeSpliceSiteVariants-class",
        "upstream",
        "upstream,FiveSpliceSiteVariants-method",
        "upstream,ThreeSpliceSiteVariants-method",
        "upstream<-",
        "upstream<-,FiveSpliceSiteVariants-method",
        "upstream<-,ThreeSpliceSiteVariants-method"
      ]
    },
    {
      "page": "WeightMatrix-class",
      "title": "Weight matrix class",
      "topics": [
        "conservedPositions",
        "conservedPositions,WeightMatrix-method",
        "readWm",
        "show,WeightMatrix-method",
        "WeightMatrix",
        "WeightMatrix-class",
        "width,WeightMatrix-method",
        "wmFilename",
        "wmFilename,WeightMatrix-method",
        "wmLocations",
        "wmLocations,WeightMatrix-method",
        "wmLocations<-",
        "wmLocations<-,WeightMatrix,character-method",
        "wmLocations<-,WeightMatrix-method",
        "wmName",
        "wmName,WeightMatrix-method",
        "wmScore",
        "wmScore,character,character-method",
        "wmScore,character,DNAStringSet-method",
        "wmScore,WeightMatrix,character-method",
        "wmScore,WeightMatrix,DNAStringSet-method",
        "wmStrictLocations",
        "wmStrictLocations,WeightMatrix-method",
        "wmStrictLocations<-",
        "wmStrictLocations<-,WeightMatrix,logical-method",
        "wmStrictLocations<-,WeightMatrix-method"
      ]
    },
    {
      "page": "xLinked",
      "title": "X-Linked inheritance analysis",
      "topics": [
        "xLinked",
        "xLinked,VariantFilteringParam-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/VariantFiltering/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "AnnotationHub",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "biomaRt",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
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    "cpp11",
    "crayon",
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    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "deldir",
    "dichromat",
    "digest",
    "dir.expiry",
    "dplyr",
    "DT",
    "ensembldb",
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    "filelock",
    "fontawesome",
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    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GenomicScores",
    "ggplot2",
    "glue",
    "graph",
    "gridExtra",
    "gtable",
    "Gviz",
    "h5mread",
    "HDF5Array",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httpuv",
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    "jsonlite",
    "KEGGREST",
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    "mime",
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    "openssl",
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    "pillar",
    "pkgconfig",
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    "rstudioapi",
    "rtracklayer",
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    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "shinyjs",
    "shinythemes",
    "shinyTree",
    "snow",
    "sourcetools",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "usingVariantFiltering.Rnw",
      "filename": "usingVariantFiltering.pdf",
      "title": "VariantFiltering: filter coding and non-coding genetic variants",
      "engine": "utils::Sweave",
      "headings": [
        "1 Overview",
        "2 Setting up the analysis",
        "3 Annotating variants",
        "4 Filters and cutoffs",
        "5 Inheritance models",
        "6 Create a report from the filtered variants",
        "7 Using the package with parallel execution",
        "8 Session information"
      ],
      "created": "2014-03-31 17:57:37",
      "modified": "2020-09-07 15:03:32",
      "commits": 23
    }
  ],
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