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      "title": "GenomicInteractions",
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      "topics": [
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      "topics": [
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        "calculateDistances,GInteractions-method"
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      "topics": [
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      "title": "Summarise interactions between defined anchors",
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        "countsBetweenAnchors,GInteractions,GRanges-method"
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        "export.bed12,GInteractions-method"
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        "export.chiasig,GInteractions-method"
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    },
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      "topics": [
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        "export.igraph,GInteractions-method"
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      "page": "GenomicInteractions",
      "title": "Function to create a GenomicInteractions object",
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        "GenomicInteractions,ANY,ANY,ANY-method",
        "GenomicInteractions,GInteractions,ANY,ANY-method",
        "GenomicInteractions,GInteractions,numeric,ANY-method",
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      "page": "GenomicInteractions-class",
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      "topics": [
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        "description,GInteractions-method",
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        "interactionCounts",
        "interactionCounts,GInteractions-method",
        "name",
        "name,GInteractions-method"
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    },
    {
      "page": "hg19.refseq.transcripts",
      "title": "Human Refseq transcripts from chr 17-18",
      "topics": [
        "hg19.refseq.transcripts"
      ]
    },
    {
      "page": "hic_example_data",
      "title": "Example HiC dataset",
      "topics": [
        "hic_example_data"
      ]
    },
    {
      "page": "InteractionTrack",
      "title": "Constructor to create an InteractionTrack object",
      "topics": [
        "InteractionTrack"
      ]
    },
    {
      "page": "InteractionTrack-class",
      "title": "A class to hold chromatin interaction data for a specific genomic region",
      "topics": [
        "chromosome,InteractionTrack-method",
        "end,InteractionTrack-method",
        "InteractionTrack-class",
        "start,InteractionTrack-method",
        "subset,InteractionTrack-method"
      ]
    },
    {
      "page": "InteractionHelpers",
      "title": "Interaction Type Helpers",
      "topics": [
        "InteractionHelpers",
        "is.cis",
        "is.cis,GInteractions-method",
        "is.dd",
        "is.dd,GInteractions-method",
        "is.dt",
        "is.dt,GInteractions-method",
        "is.pd",
        "is.pd,GInteractions-method",
        "is.pp",
        "is.pp,GInteractions-method",
        "is.pt",
        "is.pt,GInteractions-method",
        "is.trans",
        "is.trans,GInteractions-method",
        "is.tt",
        "is.tt,GInteractions-method",
        "isInteractionType",
        "isInteractionType,GInteractions-method"
      ]
    },
    {
      "page": "makeGenomicInteractionsFromFile",
      "title": "Function to create GenomicInteraction objects from a file",
      "topics": [
        "makeGenomicInteractionsFromFile"
      ]
    },
    {
      "page": "mm9_refseq_promoters",
      "title": "Mouse Refseq promoters from chr 14-15",
      "topics": [
        "mm9_refseq_promoters"
      ]
    },
    {
      "page": "plotAvgViewpoint",
      "title": "Plot coverage around a set of virtual 4C viewpoints",
      "topics": [
        "plotAvgViewpoint"
      ]
    },
    {
      "page": "plotCisTrans",
      "title": "Plots the percentages of cis and trans interactions for a GInteractions object as a donut plot.",
      "topics": [
        "plotCisTrans"
      ]
    },
    {
      "page": "plotCounts",
      "title": "Plot a bar chart of the number of interactions supported by different numbers of reads in your data.",
      "topics": [
        "plotCounts"
      ]
    },
    {
      "page": "plotDists",
      "title": "Plots a histogram of interaction distances for a GInteractions Object",
      "topics": [
        "plotDists"
      ]
    },
    {
      "page": "plotInteractionAnnotations",
      "title": "Plot a donut plot of interaction types for an annotated GInteractions object",
      "topics": [
        "plotInteractionAnnotations"
      ]
    },
    {
      "page": "plotSummaryStats",
      "title": "Plot summary statistics for a GInteractions object",
      "topics": [
        "plotSummaryStats"
      ]
    },
    {
      "page": "plotViewpoint",
      "title": "Plot coverage around a virtual 4C viewpoint",
      "topics": [
        "plotViewpoint"
      ]
    },
    {
      "page": "removeDups",
      "title": "Remove all but one occurences of a duplicated interaction",
      "topics": [
        "removeDups"
      ]
    },
    {
      "page": "resetAnnotations",
      "title": "Reset annotations made to a GInteractions object",
      "topics": [
        "resetAnnotations",
        "resetAnnotations,GInteractions-method"
      ]
    },
    {
      "page": "sameStrand",
      "title": "Tests whether anchors have the same strand.",
      "topics": [
        "sameStrand"
      ]
    },
    {
      "page": "setters",
      "title": "Functions to set data held in a GInteractions object.",
      "topics": [
        "description<-,GInteractions,ANY-method",
        "interactionCounts<-",
        "interactionCounts<-,GInteractions-method",
        "name<-",
        "name<-,GInteractions-method",
        "setters"
      ]
    },
    {
      "page": "GInteractions-subsetByFeatures-methods",
      "title": "Subset a GInteractions object by features",
      "topics": [
        "subsetByFeatures",
        "subsetByFeatures,GInteractions,character,character-method",
        "subsetByFeatures,GInteractions,GRanges,missing-method",
        "subsetByFeatures,GInteractions,GRangesList,missing-method"
      ]
    },
    {
      "page": "sum-GInteractions-method",
      "title": "Return the total number of interactions in a GInteractions GIObject",
      "topics": [
        "sum,GInteractions-method"
      ]
    },
    {
      "page": "summariseByFeaturePairs",
      "title": "Summarise the number of interactions between two sets of features.",
      "topics": [
        "summariseByFeaturePairs",
        "summariseByFeaturePairs,GInteractions-method"
      ]
    },
    {
      "page": "summariseByFeatures",
      "title": "Summary statistics of interactions for a given feature set",
      "topics": [
        "summariseByFeatures",
        "summariseByFeatures,GInteractions-method"
      ]
    },
    {
      "page": "thymus_enh",
      "title": "Putative enhancers from mouse thymus data",
      "topics": [
        "thymus_enh"
      ]
    },
    {
      "page": "updateObject-GenomicInteractions-method",
      "title": "updateObject method for GenomicInteractions 1.3.7 and earlier",
      "topics": [
        "updateObject,GenomicInteractions-method"
      ]
    },
    {
      "page": "viewPoint",
      "title": "Virtual 4C viewpoint",
      "topics": [
        "viewPoint"
      ]
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      "source": "chiapet_vignette.rmd",
      "filename": "chiapet_vignette.html",
      "title": "Package Vignette for Genomic Interactions: ChIA-PET data",
      "author": "Malcolm Perry",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Imports",
        "Data",
        "GenomicInteractions Objects",
        "Annotation",
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      "created": "2014-10-03 23:09:29",
      "modified": "2020-04-13 13:56:45",
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      "source": "hic_vignette.Rmd",
      "filename": "hic_vignette.html",
      "title": "HiC vignette for GenomicInteractions package",
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