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  "Title": "Investigates Allele Specific Expression",
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  "Author": "Jesper R Gadin, Lasse Folkersen",
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  "Description": "Provides a framework for allelic specific expression\ninvestigation using RNA-seq data.",
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        "AllelicImbalance"
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      "topics": [
        "DetectedAI-plot",
        "detectedAI_vs_threshold_variable_multigraph_plot",
        "detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI-method",
        "detectedAI_vs_threshold_variable_plot",
        "detectedAI_vs_threshold_variable_plot,DetectedAI-method",
        "frequency_vs_threshold_variable_multigraph_plot",
        "frequency_vs_threshold_variable_multigraph_plot,DetectedAI-method",
        "frequency_vs_threshold_variable_plot",
        "frequency_vs_threshold_variable_plot,DetectedAI-class",
        "frequency_vs_threshold_variable_plot,DetectedAI-method",
        "reference_frequency_density_vs_threshold_variable_multigraph_plot",
        "reference_frequency_density_vs_threshold_variable_multigraph_plot,DetectedAI-method",
        "reference_frequency_density_vs_threshold_variable_plot",
        "reference_frequency_density_vs_threshold_variable_plot,DetectedAI-method"
      ]
    },
    {
      "page": "DetectedAI-summary",
      "title": "DetectedAI summary",
      "topics": [
        "DetectedAI-summary",
        "detectedAI_vs_threshold_variable_summary",
        "detectedAI_vs_threshold_variable_summary,DetectedAI-method",
        "frequency_vs_threshold_variable_summary",
        "frequency_vs_threshold_variable_summary,DetectedAI-method",
        "usedSNPs_vs_threshold_variable_summary",
        "usedSNPs_vs_threshold_variable_summary,DetectedAI-method"
      ]
    },
    {
      "page": "fractionPlotDf",
      "title": "Plot Dataframe",
      "topics": [
        "fractionPlotDf",
        "fractionPlotDf,ASEset-method"
      ]
    },
    {
      "page": "gba",
      "title": "global analysis wrapper",
      "topics": [
        "gba",
        "gba,character-method"
      ]
    },
    {
      "page": "genomatrix",
      "title": "genomatrix object",
      "topics": [
        "genomatrix"
      ]
    },
    {
      "page": "genotype2phase",
      "title": "genotype2phase",
      "topics": [
        "genotype2phase",
        "genotype2phase,matrix-method"
      ]
    },
    {
      "page": "getAlleleCounts",
      "title": "snp count data",
      "topics": [
        "getAlleleCounts",
        "getAlleleCounts,GAlignmentsList-method"
      ]
    },
    {
      "page": "getAlleleQuality",
      "title": "snp quality data",
      "topics": [
        "getAlleleQuality",
        "getAlleleQuality,GAlignmentsList-method"
      ]
    },
    {
      "page": "getAreaFromGeneNames",
      "title": "Get Gene Area",
      "topics": [
        "getAreaFromGeneNames",
        "getAreaFromGeneNames,character-method"
      ]
    },
    {
      "page": "getDefaultMapBiasExpMean",
      "title": "Map Bias",
      "topics": [
        "getDefaultMapBiasExpMean",
        "getDefaultMapBiasExpMean,ANY-method",
        "getDefaultMapBiasExpMean,list-method",
        "getDefaultMapBiasExpMean3D",
        "getDefaultMapBiasExpMean3D,ANY-method"
      ]
    },
    {
      "page": "getSnpIdFromLocation",
      "title": "Get rsIDs from locations of SNP",
      "topics": [
        "getSnpIdFromLocation",
        "getSnpIdFromLocation,GRanges-method"
      ]
    },
    {
      "page": "GlobalAnalysis-class",
      "title": "GlobalAnalysis class",
      "topics": [
        "GlobalAnalysis",
        "GlobalAnalysis-class",
        "GlobalAnalysis-method"
      ]
    },
    {
      "page": "GRvariants",
      "title": "GRvariants object",
      "topics": [
        "GRvariants"
      ]
    },
    {
      "page": "histplot",
      "title": "histogram plots",
      "topics": [
        "hist",
        "hist,ASEset-method",
        "hist,ReferenceBias-method",
        "histplot"
      ]
    },
    {
      "page": "implodeList-old",
      "title": "implode list of arguments into environment",
      "topics": [
        "implodeList.old"
      ]
    },
    {
      "page": "import-bam",
      "title": "Import Bam",
      "topics": [
        "impBamGAL",
        "impBamGAL,character-method",
        "import-bam"
      ]
    },
    {
      "page": "import-bam-2",
      "title": "Import Bam-2",
      "topics": [
        "impBamGRL",
        "impBamGRL.old",
        "import-bam-2"
      ]
    },
    {
      "page": "import-bcf",
      "title": "Import Bcf Selection",
      "topics": [
        "impBcfGR",
        "impBcfGR,character-method",
        "impBcfGRL",
        "impBcfGRL,character-method",
        "import-bcf"
      ]
    },
    {
      "page": "inferAlleles",
      "title": "inference of SNPs of ASEset",
      "topics": [
        "inferAlleles",
        "inferAlleles,ASEset-method"
      ]
    },
    {
      "page": "inferAltAllele",
      "title": "inferAltAllele",
      "topics": [
        "inferAltAllele",
        "inferAltAllele,ASEset-method"
      ]
    },
    {
      "page": "inferGenotypes",
      "title": "infererence of genotypes from ASEset count data",
      "topics": [
        "inferGenotypes",
        "inferGenotypes,ASEset-method"
      ]
    },
    {
      "page": "initialize-ASEset",
      "title": "Initialize ASEset",
      "topics": [
        "ASEsetFromArrays",
        "ASEsetFromCountList",
        "initialize-ASEset"
      ]
    },
    {
      "page": "initialize-DetectedAI",
      "title": "Initialize DetectedAI",
      "topics": [
        "DetectedAIFromArray",
        "initialize-DetectedAI"
      ]
    },
    {
      "page": "initialize-GlobalAnalysis",
      "title": "Initialize GlobalAnalysis",
      "topics": [
        "GAnalysis",
        "initialize-GlobalAnalysis"
      ]
    },
    {
      "page": "initialize-RiskVariant",
      "title": "Initialize RiskVariant",
      "topics": [
        "initialize-RiskVariant",
        "RiskVariantFromGRangesAndPhaseArray"
      ]
    },
    {
      "page": "legendBarplot",
      "title": "add legend to AllelicImbalance barplot",
      "topics": [
        "legendBarplot"
      ]
    },
    {
      "page": "LinkVariantAlmlof-class",
      "title": "LinkVariantAlmlof class",
      "topics": [
        "LinkVariantAlmlof",
        "LinkVariantAlmlof-class",
        "LinkVariantAlmlof-method",
        "pvalue",
        "pvalue,LinkVariantAlmlof-method"
      ]
    },
    {
      "page": "LinkVariantAlmlof-plot",
      "title": "plot LinkVariantAlmlof objects",
      "topics": [
        "LinkVariantAlmlof-plot",
        "plot",
        "plot,LinkVariantAlmlof,ANY-method",
        "plot,LinkVariantAlmlof-method"
      ]
    },
    {
      "page": "lva",
      "title": "lva",
      "topics": [
        "lva",
        "lva,array-method",
        "lva,ASEset-method"
      ]
    },
    {
      "page": "lva.internal",
      "title": "lva.internal",
      "topics": [
        "lva.internal",
        "lva.internal,array-method"
      ]
    },
    {
      "page": "makeMaskedFasta",
      "title": "makes masked fasta reference",
      "topics": [
        "makeMaskedFasta",
        "makeMaskedFasta,character-method"
      ]
    },
    {
      "page": "mapBiasRef",
      "title": "mapBias for reference allele",
      "topics": [
        "mapBiasRef",
        "mapBiasRef,ASEset-method"
      ]
    },
    {
      "page": "minCountFilt",
      "title": "minCountFilt methods",
      "topics": [
        "minCountFilt",
        "minCountFilt,ASEset-method"
      ]
    },
    {
      "page": "minFreqFilt",
      "title": "minFreqFilt methods",
      "topics": [
        "minFreqFilt",
        "minfreqFilt",
        "minFreqFilt,ASEset-method"
      ]
    },
    {
      "page": "multiAllelicFilt",
      "title": "multi-allelic filter methods",
      "topics": [
        "multiAllelicFilt",
        "multiAllelicFilt,ASEset-method"
      ]
    },
    {
      "page": "phase2genotype",
      "title": "phase2genotype",
      "topics": [
        "phase2genotype",
        "phase2genotype,array-method"
      ]
    },
    {
      "page": "phaseArray2phaseMatrix",
      "title": "phaseArray2phaseMatrix",
      "topics": [
        "phaseArray2phaseMatrix",
        "phaseArray2phaseMatrix,array-method"
      ]
    },
    {
      "page": "phaseMatrix2Array",
      "title": "phaseMatrix2Array",
      "topics": [
        "phaseMatrix2Array",
        "phaseMatrix2Array,matrix-method"
      ]
    },
    {
      "page": "randomRef",
      "title": "Random ref allele from genotype",
      "topics": [
        "randomRef",
        "randomRef,ASEset-method"
      ]
    },
    {
      "page": "reads",
      "title": "reads object",
      "topics": [
        "reads"
      ]
    },
    {
      "page": "refAllele",
      "title": "Reference allele",
      "topics": [
        "refAllele",
        "refAllele,ASEset-method"
      ]
    },
    {
      "page": "regionSummary",
      "title": "regionSummary",
      "topics": [
        "regionSummary",
        "regionSummary,ASEset-method",
        "regionSummary,numeric-method"
      ]
    },
    {
      "page": "RegionSummary-class",
      "title": "RegionSummary class",
      "topics": [
        "basic",
        "basic,RegionSummary-method",
        "RegionSummary",
        "RegionSummary-class",
        "RegionSummary-method",
        "sumnames",
        "sumnames,RegionSummary-method"
      ]
    },
    {
      "page": "RiskVariant-class",
      "title": "RiskVariant class",
      "topics": [
        "alt,RiskVariant-method",
        "alt<-,RiskVariant,ANY-method",
        "phase,RiskVariant-method",
        "phase<-,RiskVariant-method",
        "ref,RiskVariant-method",
        "ref<-,RiskVariant,ANY-method",
        "RiskVariant",
        "RiskVariant-class",
        "RiskVariant-method"
      ]
    },
    {
      "page": "scanForHeterozygotes-old",
      "title": "scanForHeterozygotes-old",
      "topics": [
        "scanForHeterozygotes.old"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/AllelicImbalance/raw/HEAD/README.md",
  "_rundeps": [
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    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
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    "tinytex",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
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    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "AllelicImbalance-vignette.Rmd",
      "filename": "AllelicImbalance-vignette.html",
      "title": "AllelicImbalance Vignette",
      "author": "Jesper R. Gadin and Lasse Folkersen",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ASEset",
        "Simple example of building an ASEset object",
        "Building an ASEset object using Bcf or Vcf files",
        "Using strand information",
        "Two useful helper functions",
        "Adding phenotype data",
        "Adding genotype information",
        "Adding phase information",
        "Adding reference and alternative allele information",
        "Tests",
        "Statistical analysis of an ASEset object",
        "Summary functions",
        "Base graphics",
        "Plotting of an ASEset object",
        "Plot with annotation",
        "locationplot",
        "Grid graphics",
        "gbarplot",
        "glocationplot",
        "Custom location plots",
        "Important notifications",
        "Update old objects",
        "Conclusion",
        "Links",
        "Session Info"
      ],
      "created": "2015-03-16 10:45:13",
      "modified": "2017-04-29 20:08:41",
      "commits": 21
    }
  ],
  "_score": 5.079181246047625,
  "_indexed": true,
  "_nocasepkg": "allelicimbalance",
  "_universes": [
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    "pappewaio"
  ],
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