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"title": "glocationplot ASEset objects", "topics": [ "ASEset-glocationplot", "glocationplot", "glocationplot,ASEset-method" ] }, { "page": "ASEset-gviztrack", "title": "ASEset-gviztrack ASEset objects", "topics": [ "ASEDAnnotationTrack", "ASEDAnnotationTrack,ASEset-method", "ASEset-gviztrack", "CoverageDataTrack", "CoverageDataTrack,ASEset-method" ] }, { "page": "locationplot", "title": "locationplot ASEset objects", "topics": [ "ASEset-locationplot", "locationplot", "locationplot,ASEset-method" ] }, { "page": "ASEset-scanForHeterozygotes", "title": "scanForHeterozygotes", "topics": [ "ASEset-scanForHeterozygotes", "scanForHeterozygotes", "scanForHeterozygotes,ASEset-method", "scanForHeterozygotes,GAlignmentsList-method" ] }, { "page": "ASEset.old", "title": "ASEset.old object", "topics": [ "ASEset.old" ] }, { "page": "ASEset.sim", "title": "ASEset.sim object", "topics": [ "ASEset.sim" ] }, { "page": "ASEsetFromBam", "title": "ASEset from bam file", "topics": [ "ASEsetFromBam", "ASEsetFromBam,GRanges-method" ] }, { "page": "barplot-lattice-support", "title": "lattice barplot inner functions for ASEset objects", "topics": [ "barplot-lattice-support", "barplotLatticeCounts", "barplotLatticeFraction" ] }, { "page": "binom.test", "title": "binomial test", "topics": [ "binom.test", "binom.test,ASEset-method" ] }, { "page": "chisq.test", "title": "chi-square test", "topics": [ "chisq.test", "chisq.test,ASEset-method" ] }, { "page": "countAllelesFromBam", "title": "alleleCounts from bam file", "topics": [ "countAllelesFromBam", "countAllelesFromBam,GRanges-method" ] }, { "page": "coverageMatrixListFromGAL", "title": "coverage matrix of GAlignmentsList", "topics": [ "coverageMatrixListFromGAL", "coverageMatrixListFromGAL,GAlignmentsList-method" ] }, { "page": "defaultMapBias", "title": "Generate default mapbias from genotype", "topics": [ "defaultMapBias", "defaultMapBias,ASEset-method" ] }, { "page": "defaultPhase", "title": "defaultPhase", "topics": [ "defaultPhase", "defaultPhase,numeric-method" ] }, { "page": "detectAI", "title": "detectAI", "topics": [ "detectAI", "detectAI,ASEset-method" ] }, { "page": "DetectedAI-class", "title": "DetectedAI class", "topics": [ "DetectedAI", "DetectedAI-class", "DetectedAI-method", "referenceFrequency", "referenceFrequency,DetectedAI-method", "thresholdCountSample", "thresholdCountSample,DetectedAI-method", "thresholdDeltaFrequency", "thresholdDeltaFrequency,DetectedAI-method", "thresholdFrequency", "thresholdFrequency,DetectedAI-method", "thresholdPvalue", "thresholdPvalue,DetectedAI-method" ] }, { "page": "DetectedAI-plot", "title": "DetectedAI plot", "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": 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