Files in pappewaio/AllelicImbalance

Investigates Allele Specific Expression

R/ASEset-class.R R/AllelicImbalance-package.R R/DetectedAI-class.R R/GlobalAnalysis-class.R R/GvizTrack-methods.R R/LinkVariantAlmlof-class.R R/RegionSummary-class.R R/RiskVariant-class.R R/auxillary-functions-annotation.R R/auxillary-functions-visuals.R R/auxillary-methods-summaries.R R/auxillary-methods.R R/barplot-methods.R R/binom.test-methods.R R/boxplot-methods.R R/chisq.test-methods.R R/deprecations.R R/detect-methods.R R/filter-methods.R R/histplot-methods.R R/inference-methods.R R/initialize-methods.R R/linkage-methods.R R/list-methods.R R/locationplot-methods.R R/mapbias-methods.R R/plot-methods.R R/show-methods.R R/simulation-methods.R R/summary-methods.R R/utils.R README.md man/ASEset-barplot.Rd man/ASEset-class.Rd man/ASEset-filters.Rd man/ASEset-gbarplot.Rd man/ASEset-glocationplot.Rd man/ASEset-gviztrack.Rd man/ASEset-scanForHeterozygotes.Rd man/ASEset.old.Rd man/ASEset.sim.Rd man/ASEsetFromBam.Rd man/AllelicImbalance-package.Rd man/DetectedAI-class.Rd man/DetectedAI-plot.Rd man/DetectedAI-summary.Rd man/GRvariants.Rd man/GlobalAnalysis-class.Rd man/LinkVariantAlmlof-class.Rd man/LinkVariantAlmlof-plot.Rd man/RegionSummary-class.Rd man/RiskVariant-class.Rd man/annotation-wrappers.Rd man/annotationBarplot.Rd man/barplot-lattice-support.Rd man/binom.test.Rd man/chisq.test.Rd man/cigar-utilities.Rd man/countAllelesFromBam.Rd man/coverageMatrixListFromGAL.Rd man/decorateWithExons.Rd man/decorateWithGenes.Rd man/defaultMapBias.Rd man/defaultPhase.Rd man/detectAI.Rd man/fractionPlotDf.Rd man/gba.Rd man/genomatrix.Rd man/genotype2phase.Rd man/getAlleleCounts.Rd man/getAlleleQuality.Rd man/getAreaFromGeneNames.Rd man/getDefaultMapBiasExpMean.Rd man/getSnpIdFromLocation.Rd man/histplot.Rd man/implodeList-old.Rd man/import-bam-2.Rd man/import-bam.Rd man/import-bcf.Rd man/inferAlleles.Rd man/inferAltAllele.Rd man/inferGenotypes.Rd man/initialize-ASEset.Rd man/initialize-DetectedAI.Rd man/initialize-GlobalAnalysis.Rd man/initialize-RiskVariant.Rd man/legendBarplot.Rd man/locationplot.Rd man/lva.Rd man/lva.internal.Rd man/makeMaskedFasta.Rd man/mapBiasRef.Rd man/minCountFilt.Rd man/minFreqFilt.Rd man/multiAllelicFilt.Rd man/phase2genotype.Rd man/phaseArray2phaseMatrix.Rd man/phaseMatrix2Array.Rd man/randomRef.Rd man/reads.Rd man/refAllele.Rd man/regionSummary.Rd man/scanForHeterozygotes-old.Rd tests/test-all.R tests/testthat/test_calc_arank.R tests/testthat/test_calc_frequency.R tests/testthat/test_cigar_utility.R tests/testthat/test_detectAI.R tests/testthat/test_filters.R tests/testthat/test_fraction.R tests/testthat/test_frequency.R tests/testthat/test_genotype2phase.R tests/testthat/test_import_counts.R tests/testthat/test_infer_alleles.R tests/testthat/test_infer_genotypes.R tests/testthat/test_lva.R tests/testthat/test_phase.R tests/testthat/test_phase2genotype.R tests/testthat/test_phaseArray2phaseMatrix.R tests/testthat/test_refFraction.R tests/testthat/test_regionSummary.R tests/testthat/test_utils.R vignettes/AllelicImbalance-vignette.Rmd