Files in pappewaio/AllelicImbalance
Investigates Allele Specific Expression
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
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-annotation.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
data/ASEset.rdata
data/ASEset.sim.rdata
data/GRvariants.rdata
data/genomatrix.rdata
data/reads.rdata
inst/CITATION
inst/extdata/ERP000101_subset/ERP000101.bcf
inst/extdata/ERP000101_subset/ERP000101.bcf.csi
inst/extdata/ERP000101_subset/ERP000101.vcf
inst/extdata/ERP000101_subset/ERR009097.bam
inst/extdata/ERP000101_subset/ERR009097.bam.bai
inst/extdata/ERP000101_subset/ERR009102.bam
inst/extdata/ERP000101_subset/ERR009102.bam.bai
inst/extdata/ERP000101_subset/ERR009103.bam
inst/extdata/ERP000101_subset/ERR009103.bam.bai
inst/extdata/ERP000101_subset/ERR009113.bam
inst/extdata/ERP000101_subset/ERR009113.bam.bai
inst/extdata/ERP000101_subset/ERR009115.bam
inst/extdata/ERP000101_subset/ERR009115.bam.bai
inst/extdata/ERP000101_subset/ERR009122.bam
inst/extdata/ERP000101_subset/ERR009122.bam.bai
inst/extdata/ERP000101_subset/ERR009126.bam
inst/extdata/ERP000101_subset/ERR009126.bam.bai
inst/extdata/ERP000101_subset/ERR009127.bam
inst/extdata/ERP000101_subset/ERR009127.bam.bai
inst/extdata/ERP000101_subset/ERR009129.bam
inst/extdata/ERP000101_subset/ERR009129.bam.bai
inst/extdata/ERP000101_subset/ERR009135.bam
inst/extdata/ERP000101_subset/ERR009135.bam.bai
inst/extdata/ERP000101_subset/ERR009141.bam
inst/extdata/ERP000101_subset/ERR009141.bam.bai
inst/extdata/ERP000101_subset/ERR009142.bam
inst/extdata/ERP000101_subset/ERR009142.bam.bai
inst/extdata/ERP000101_subset/ERR009144.bam
inst/extdata/ERP000101_subset/ERR009144.bam.bai
inst/extdata/ERP000101_subset/ERR009146.bam
inst/extdata/ERP000101_subset/ERR009146.bam.bai
inst/extdata/ERP000101_subset/ERR009147.bam
inst/extdata/ERP000101_subset/ERR009147.bam.bai
inst/extdata/ERP000101_subset/ERR009154.bam
inst/extdata/ERP000101_subset/ERR009154.bam.bai
inst/extdata/ERP000101_subset/ERR009157.bam
inst/extdata/ERP000101_subset/ERR009157.bam.bai
inst/extdata/ERP000101_subset/ERR009159.bam
inst/extdata/ERP000101_subset/ERR009159.bam.bai
inst/extdata/ERP000101_subset/ERR009160.bam
inst/extdata/ERP000101_subset/ERR009160.bam.bai
inst/extdata/ERP000101_subset/ERR009167.bam
inst/extdata/ERP000101_subset/ERR009167.bam.bai
inst/extdata/hg19.chr17.subset.fa
inst/extdata/hg19.chr17.subset.fa.fai
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
