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
Package: AllelicImbalance 1.51.0
Jesper R Gadin
AllelicImbalance: Investigates Allele Specific Expression
Provides a framework for allelic specific expression investigation using RNA-seq data.
Authors:
AllelicImbalance_1.51.0.tar.gz
AllelicImbalance_1.51.0.zip(r-4.7)AllelicImbalance_1.51.0.zip(r-4.6)AllelicImbalance_1.51.0.zip(r-4.5)
AllelicImbalance_1.51.0.tgz(r-4.6-any)AllelicImbalance_1.51.0.tgz(r-4.5-any)
AllelicImbalance_1.51.0.tar.gz(r-4.7-any)AllelicImbalance_1.51.0.tar.gz(r-4.6-any)
AllelicImbalance_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AllelicImbalance/json (API)
| # Install 'AllelicImbalance' in R: |
| install.packages('AllelicImbalance', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pappewaio/allelicimbalance/issues
Datasets:
- ASEset - ASEset objects
- ASEset.sim - ASEset.sim object
- genomatrix - Genomatrix object
- GRvariants - GRvariants object
- reads - Reads object
On BioConductor:AllelicImbalance-1.51.0(bioc 3.24)AllelicImbalance-1.50.0(bioc 3.23)
geneticsinfrastructuresequencing
Last updated from:718ddd46b7. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 350 | ||
| linux-devel-x86_64 | OK | 655 | ||
| source / vignettes | OK | 544 | ||
| linux-release-x86_64 | OK | 736 | ||
| macos-release-arm64 | OK | 457 | ||
| macos-oldrel-arm64 | OK | 376 | ||
| windows-devel | OK | 695 | ||
| windows-release | OK | 721 | ||
| windows-oldrel | OK | 560 | ||
| wasm-release | OK | 258 |
Exports:alleleCountsalleleCounts<-altalt<-altExistannotationBarplotaqualsaquals<-arankASEDAnnotationTrackASEsetFromArraysASEsetFromBamASEsetFromCountListbarplotbarplotLatticeCountsbarplotLatticeFractionbasicbinom.testchisq.testcountAllelesFromBamcountsPerSamplecountsPerSnpCoverageDataTrackcoverageMatrixListFromGALdecorateWithExonsdecorateWithGenesdefaultMapBiasdefaultPhasedetectAIdetectedAI_vs_threshold_variable_multigraph_plotdetectedAI_vs_threshold_variable_plotdetectedAI_vs_threshold_variable_summaryDetectedAIFromArrayfractionfractionPlotDffrequencyfrequency_vs_threshold_variable_multigraph_plotfrequency_vs_threshold_variable_plotfrequency_vs_threshold_variable_summaryGAnalysisgbagbarplotgenotypegenotype<-genotype2phasegetAlleleCountsgetAlleleQualitygetAnnotationDataFramegetAreaFromGeneNamesgetCDSFromAnnotationgetCDSVectorgetDefaultMapBiasExpMeangetDefaultMapBiasExpMean3DgetExonsFromAnnotationgetExonsVectorgetGenesFromAnnotationgetGenesVectorgetSnpIdFromLocationgetTranscriptsFromAnnotationgetTranscriptsVectorglocationplothetFiltimpBamGALimpBamGRLimpBcfGRimpBcfGRLimplodeList.oldinferAllelesinferAltAlleleinferGenotypeslegendBarplotlocationplotlvalva.internalmakeMaskedFastamapBiasmapBias<-mapBiasRefmaternalAlleleminCountFiltminFreqFiltmultiAllelicFiltpaternalAllelephasephase<-phase2genotypephaseArray2phaseMatrixphaseMatrix2ArrayplotpvaluerandomRefrealCigarPosition.oldrealCigarPositions.oldrealCigarPositionsList.oldrefref<-refAllelereference_frequency_density_vs_threshold_variable_multigraph_plotreference_frequency_density_vs_threshold_variable_plotreferenceFrequencyrefExistregionSummaryRiskVariantFromGRangesAndPhaseArrayscanForHeterozygotesscanForHeterozygotes.oldsumnamesthresholdCountSamplethresholdDeltaFrequencythresholdFrequencythresholdPvalueusedSNPs_vs_threshold_variable_summary
Dependencies:abindade4AnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmennetopensslpillarpixmappkgconfigpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalessegmentedSeqinfoseqinrsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A package meant to provide all basic functions for high-throughput allele specific expression analysis | AllelicImbalance-package AllelicImbalance |
| AnnotationDb wrappers | annotation-wrappers getAnnotationDataFrame getCDSFromAnnotation getCDSVector getExonsFromAnnotation getExonsVector getGenesFromAnnotation getGenesVector getTranscriptsFromAnnotation getTranscriptsVector |
| add annotation to AllelicImbalance barplot | annotationBarplot |
| barplot ASEset objects | ASEset-barplot barplot barplot,ASEset-method |
| ASEset objects | alleleCounts alleleCounts,ASEset-method alleleCounts<- alleleCounts<-,ASEset-method alt alt,ASEset-method alt<- alt<-,ASEset,ANY-method altExist altExist,ASEset-method aquals aquals,ASEset-method aquals<- aquals<-,ASEset-method arank arank,ASEset-method ASEset ASEset-class countsPerSample countsPerSample,ASEset-method countsPerSnp countsPerSnp,ASEset-method fraction fraction,ASEset-method frequency frequency,ASEset-method genotype genotype,ASEset-method genotype<- genotype<-,ASEset-method mapBias mapBias,ASEset-method mapBias<- mapBias<-,ASEset-method maternalAllele maternalAllele,ASEset-method paternalAllele paternalAllele,ASEset-method phase phase,ASEset-method phase<- phase<-,ASEset-method ref ref,ASEset-method ref<- ref<-,ASEset,ANY-method refExist refExist,ASEset-method |
| genotype filter methods | ASEset-filters hetFilt hetFilt,ASEset-method |
| gbarplot ASEset objects | ASEset-gbarplot gbarplot gbarplot,ASEset-method |
| glocationplot ASEset objects | ASEset-glocationplot glocationplot glocationplot,ASEset-method |
| ASEset-gviztrack ASEset objects | ASEDAnnotationTrack ASEDAnnotationTrack,ASEset-method ASEset-gviztrack CoverageDataTrack CoverageDataTrack,ASEset-method |
| locationplot ASEset objects | ASEset-locationplot locationplot locationplot,ASEset-method |
| scanForHeterozygotes | ASEset-scanForHeterozygotes scanForHeterozygotes scanForHeterozygotes,ASEset-method scanForHeterozygotes,GAlignmentsList-method |
| ASEset.old object | ASEset.old |
| ASEset.sim object | ASEset.sim |
| ASEset from bam file | ASEsetFromBam ASEsetFromBam,GRanges-method |
| lattice barplot inner functions for ASEset objects | barplot-lattice-support barplotLatticeCounts barplotLatticeFraction |
| binomial test | binom.test binom.test,ASEset-method |
| chi-square test | chisq.test chisq.test,ASEset-method |
| alleleCounts from bam file | countAllelesFromBam countAllelesFromBam,GRanges-method |
| coverage matrix of GAlignmentsList | coverageMatrixListFromGAL coverageMatrixListFromGAL,GAlignmentsList-method |
| Generate default mapbias from genotype | defaultMapBias defaultMapBias,ASEset-method |
| defaultPhase | defaultPhase defaultPhase,numeric-method |
| detectAI | detectAI detectAI,ASEset-method |
| DetectedAI class | 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 |
| DetectedAI plot | 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 |
| DetectedAI summary | 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 |
| Plot Dataframe | fractionPlotDf fractionPlotDf,ASEset-method |
| global analysis wrapper | gba gba,character-method |
| genomatrix object | genomatrix |
| genotype2phase | genotype2phase genotype2phase,matrix-method |
| snp count data | getAlleleCounts getAlleleCounts,GAlignmentsList-method |
| snp quality data | getAlleleQuality getAlleleQuality,GAlignmentsList-method |
| Get Gene Area | getAreaFromGeneNames getAreaFromGeneNames,character-method |
| Map Bias | getDefaultMapBiasExpMean getDefaultMapBiasExpMean,ANY-method getDefaultMapBiasExpMean,list-method getDefaultMapBiasExpMean3D getDefaultMapBiasExpMean3D,ANY-method |
| Get rsIDs from locations of SNP | getSnpIdFromLocation getSnpIdFromLocation,GRanges-method |
| GlobalAnalysis class | GlobalAnalysis GlobalAnalysis-class GlobalAnalysis-method |
| GRvariants object | GRvariants |
| histogram plots | hist hist,ASEset-method hist,ReferenceBias-method histplot |
| implode list of arguments into environment | implodeList.old |
| Import Bam | impBamGAL impBamGAL,character-method import-bam |
| Import Bam-2 | impBamGRL impBamGRL.old import-bam-2 |
| Import Bcf Selection | impBcfGR impBcfGR,character-method impBcfGRL impBcfGRL,character-method import-bcf |
| inference of SNPs of ASEset | inferAlleles inferAlleles,ASEset-method |
| inferAltAllele | inferAltAllele inferAltAllele,ASEset-method |
| infererence of genotypes from ASEset count data | inferGenotypes inferGenotypes,ASEset-method |
| Initialize ASEset | ASEsetFromArrays ASEsetFromCountList initialize-ASEset |
| Initialize DetectedAI | DetectedAIFromArray initialize-DetectedAI |
| Initialize GlobalAnalysis | GAnalysis initialize-GlobalAnalysis |
| Initialize RiskVariant | initialize-RiskVariant RiskVariantFromGRangesAndPhaseArray |
| add legend to AllelicImbalance barplot | legendBarplot |
| LinkVariantAlmlof class | LinkVariantAlmlof LinkVariantAlmlof-class LinkVariantAlmlof-method pvalue pvalue,LinkVariantAlmlof-method |
| plot LinkVariantAlmlof objects | LinkVariantAlmlof-plot plot plot,LinkVariantAlmlof,ANY-method plot,LinkVariantAlmlof-method |
| lva | lva lva,array-method lva,ASEset-method |
| lva.internal | lva.internal lva.internal,array-method |
| makes masked fasta reference | makeMaskedFasta makeMaskedFasta,character-method |
| mapBias for reference allele | mapBiasRef mapBiasRef,ASEset-method |
| minCountFilt methods | minCountFilt minCountFilt,ASEset-method |
| minFreqFilt methods | minFreqFilt minfreqFilt minFreqFilt,ASEset-method |
| multi-allelic filter methods | multiAllelicFilt multiAllelicFilt,ASEset-method |
| phase2genotype | phase2genotype phase2genotype,array-method |
| phaseArray2phaseMatrix | phaseArray2phaseMatrix phaseArray2phaseMatrix,array-method |
| phaseMatrix2Array | phaseMatrix2Array phaseMatrix2Array,matrix-method |
| Random ref allele from genotype | randomRef randomRef,ASEset-method |
| reads object | reads |
| Reference allele | refAllele refAllele,ASEset-method |
| regionSummary | regionSummary regionSummary,ASEset-method regionSummary,numeric-method |
| RegionSummary class | basic basic,RegionSummary-method RegionSummary RegionSummary-class RegionSummary-method sumnames sumnames,RegionSummary-method |
| RiskVariant class | 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 |
| scanForHeterozygotes-old | scanForHeterozygotes.old |
