Package index • ChrAccR

All functions
`DsASC-class`	DsASC Class
`DsASC()`	Create a new DsASC object
`DsASC.gatk()`	Import Allele-Specific Chromatin Data (GATK VCFs + BAM Pileup)
`DsATAC-class`	DsATAC
`DsATAC.bam()`	DsATAC.bam
`DsATAC.cellranger()`	DsATAC.cellranger
`DsATAC.fragmentBed()`	DsATAC.fragmentBed
`DsATAC.snakeATAC()`	DsATAC.snakeATAC
`DsATACsc-class`	DsATACsc
`DsATACsc.archr()`	DsATACsc.archr
`DsATACsc.fragments()`	DsATACsc.fragments
`DsAcc-class`	DsAcc
`DsNOMe-class`	DsNOMe
`DsNOMe.bisSNP()`	DsNOMe.bisSNP
`PWMatrixToProbMatrix()`	PWMatrixToProbMatrix
`addSampleAnnotCol(<DsAcc>)`	addSampleAnnotCol-methods
`aggregateRegionCounts(<DsATAC>)`	aggregateRegionCounts-methods
`annotateASCSites()`	Annotate DsASC SNPs with Consensus Peaks
`ascActivityStat()`	Allele-specific TF-activity statistic for one motif's sites
`ascAggregate()`	Aggregate ref/alt across a set of samples (columns)
`ascBestDonor()`	Best donor for a SNP: het there (per master membership) and most reads
`ascDonorDepth()`	Rank donors by sequencing depth at tested sites
`ascDropHomozygous()`	Drop homozygous / mis-genotyped sites using donor-pooled evidence
`ascFilterRegions()`	Drop ASC sites in blacklist / low-mappability regions
`ascOrientReads()`	Orient allele counts toward the predicted stronger-binding allele
`ascPoolReplicates()`	Pool technical-replicate libraries into biological samples
`ascSharing()`	Estimate shared-imbalance proportion between two count sets (ashR)
`ascSitePosterior()`	Per-site binomial posterior + FDR for a ref/alt vector
`ascStratum()`	Stratify a pair of (cellType, stimulus) groups into the 4 sharing strata
`ascTFActivity()`	Compute allele-specific TF activity for a set of samples
`ascTFActivityByDonor()`	Allele-specific TF activity computed within each donor
`ascTFActivitySwitch()`	Allele-specific TF activity across conditions, with a switch (handoff) score
`ascTFFamily()`	Assign a broad structural family to a (JASPAR) TF name
`buildMasterSNPs()`	Build a shared master heterozygous-SNP list across donors
`calcASCStatistics()`	Calculate ASC Statistics (Calderon et al. 2019)
`callPeaks(<DsATAC>)`	callPeaks-methods
`cleanMem()`	cleanMem
`colZscores()`	colZscores
`collapseMotifMatrix()`	collapseMotifMatrix
`computeDiffAcc.rnb.nome()`	computeDiffAcc.rnb.nome
`createReport_differential(<DsATAC>)`	createReport_differential-methods
`createReport_exploratory(<DsATAC>)`	createReport_exploratory-methods
`createReport_filtering(<DsATAC>)`	createReport_filtering-methods
`createReport_normalization(<DsATAC>)`	createReport_normalization-methods
`createReport_summary(<DsATAC>)`	createReport_summary-methods
`dimRed_UMAP(<DsATACsc>)`	dimRed_UMAP-methods
`estimateSharedImbalance()`	Estimate the Proportion of Shared ASC Imbalance Effects
`exportCountTracks(<DsATAC>)`	exportCountTracks-methods
`fastqDirToTable()`	fastqDirToTable
`filterASCByPeaks()`	Filter DsASC to Peak-Overlapping SNPs
`filterByGRanges(<DsATAC>)`	filterByGRanges-methods
`filterCellsTssEnrichment(<DsATACsc>)`	filterCellsTssEnrichment-methods
`filterChroms(<DsASC>)`	filterChroms-methods (DsASC)
`filterChroms(<DsATAC>)`	filterChroms-methods
`filterForRecurrence()`	Filter for Recurrent Allele-Specific Chromatin Events
`filterLowCovg(<DsASC>)`	filterLowCovg-methods (DsASC)
`filterLowCovg(<DsATAC>)`	filterLowCovg-methods
`findNearestGeneForGr()`	findNearestGeneForGr
`findOrderedNames()`	findOrderedNames
`getATACfragments()`	getATACfragments
`getAccessibility(<DsASC>)`	Get the peak-level accessibility matrix
`getChrAccRAnnotationPackage()`	getChrAccRAnnotationPackage
`getChromVarDev(<DsATAC>)`	getChromVarDev-methods
`getCiceroGeneActivities(<DsATAC>)`	getCiceroGeneActivities-methods
`getComparisonInfo()`	getComparisonInfo
`getComparisonTable(<DsAcc>)`	getComparisonTable-methods
`getConfigElement()`	getConfigElement
`getConsensusPeakSet()`	getConsensusPeakSet
`getCoord(<DsAcc>)`	getCoord-methods
`getCounts(<DsATAC>)`	getCounts-methods
`getCountsSE(<DsATAC>)`	getCountsSE-methods
`getCoverage(<DsATAC>)`	getCoverage-methods
`getCovg(<DsNOMe>)`	getCovg-methods
`getDESeq2Dataset(<DsATAC>)`	getDESeq2Dataset-methods
`getDiffAcc(<DsATAC>)`	getDiffAcc-methods
`getFragmentGr(<DsATAC>)`	getFragmentGr-methods
`getFragmentGrl(<DsATAC>)`	getFragmentGrl-methods
`getFragmentNum(<DsATAC>)`	getFragmentNum-methods
`getGenome(<DsAcc>)`	getGenome-methods
`getGenomeObject()`	getGenomeObject
`getGroupsFromTable()`	getGroupsFromTable
`getInsertionKmerFreq(<DsATAC>)`	getInsertionKmerFreq-methods
`getInsertionSites(<DsATAC>)`	getInsertionSites-methods
`getJasparAnnot()`	getJasparAnnot
`getJasparSymbols()`	getJasparSymbols
`getMeth(<DsNOMe>)`	getMeth-methods
`getMonocleCellDataSet(<DsATAC>)`	getMonocleCellDataSet-methods
`getMotifClustering()`	getMotifClustering
`getMotifDistMat()`	getMotifDistMat
`getMotifDistMat.jaspar()`	getMotifDistMat.jaspar
`getMotifEnrichment(<DsATAC>)`	getMotifEnrichment-methods
`getMotifFootprints(<DsATAC>)`	getMotifFootprints-methods
`getMotifOccurrences()`	getMotifOccurrences
`getNRegions(<DsAcc>)`	getNRegions-methods
`getNonOverlappingByScore()`	getNonOverlappingByScore
`getPeakSet.snakeATAC()`	getPeakSet.snakeATAC
`getPeaks(<DsASC>)`	Get peak coordinates
`getQuickTssEnrichment(<DsATAC>)`	getQuickTssEnrichment-methods
`getRegionMapping(<DsNOMe>)`	getRegionMapping-methods
`getRegionTypes(<DsAcc>)`	getRegionTypes-methods
`getSampleAnnot(<DsAcc>)`	getSampleAnnot-methods
`getSampleMetrics.snakeATAC()`	getSampleMetrics.snakeATAC
`getSamples(<DsAcc>)`	getSamples-methods
`getScQcStatsTab(<DsATACsc>)`	getScQcStatsTab-methods
`getTfAnnot()`	getTfAnnot
`getTssEnrichment(<DsATAC>)`	getTssEnrichment-methods
`getTssEnrichmentBatch(<DsATAC>)`	getTssEnrichmentBatch-methods
`hmSeqLogo()`	hmSeqLogo
`isCanonicalChrom()`	isCanonicalChrom
`iterativeLSI(<DsATACsc>)`	iterativeLSI-methods
`join(<DsATAC>)`	join-methods
`length(<DsAcc>)`	Retrieve the number of samples contained in a DsAcc object
`loadConfig()`	loadConfig
`loadDsAcc()`	loadDsAcc
`maskMethNA(<DsNOMe>)`	maskMethNA-methods
`mergeDsASCArray()`	Merge per-cell-type DsASC objects into unified count matrices
`mergePseudoBulk(<DsATACsc>)`	mergePseudoBulk-methods
`mergeSamples(<DsATAC>)`	mergeSamples-methods
`mergeStrands(<DsNOMe>)`	mergeStrands-methods
`normalizeMeth(<DsNOMe>)`	normalizeMeth-methods
`plotASCBalance()`	Plot allele-specific chromatin balance across samples (Fig 4a style)
`plotASCManhattan()`	Manhattan-style plot of ASC significance along the genome
`plotASCTFActivity()`	Lollipop / dot plot of allele-specific TF activity across contexts
`plotASCTFActivityScatter()`	Resting-vs-stimulated allele-specific TF activity scatter
`plotASCTFDonorDelta()`	Per-donor robustness of the stimulation effect
`plotASCVolcano()`	Volcano plot of ASC effect size vs significance
`plotInsertSizeDistribution(<DsATAC>)`	plotInsertSizeDistribution-methods
`prepareMotifmatchr()`	prepareMotifmatchr
`projectMatrix_UMAP()`	projectMatrix_UMAP
`readMACS2peakFile()`	readMACS2peakFile
`regionAggregation(<DsATAC>)`	regionAggregation-methods
`regionAggregation(<DsNOMe>)`	regionAggregation-methods
`regionSetCounts(<DsATAC>)`	regionSetCounts-methods
`removeFragmentData(<DsATAC>)`	removeFragmentData-methods
`removeRegionData(<DsATAC>)`	removeRegionData-methods
`removeRegionType(<DsATAC>)`	removeRegionType-methods
`removeRegions(<DsATAC>)`	removeRegions-methods
`removeRegions(<DsAcc>)`	removeRegions-methods
`removeRegions(<DsNOMe>)`	removeRegions-methods
`removeSamples(<DsATAC>)`	removeSamples-methods
`rowZscores()`	rowZscores
`run_atac()`	run_atac
`run_atac_chromvar()`	run_atac_chromvar
`run_atac_differential()`	run_atac_differential
`run_atac_exploratory()`	run_atac_exploratory
`run_atac_filtering()`	run_atac_filtering
`run_atac_normalization()`	run_atac_normalization
`run_atac_peakcalling()`	run_atac_peakcalling
`run_atac_qc()`	run_atac_qc
`run_atac_sc_unsupervised()`	run_atac_sc_unsupervised
`safeMatrixStats()`	safeMatrixStats
`samplePseudoBulk(<DsATACsc>)`	samplePseudoBulk-methods
`saveConfig()`	saveConfig
`saveDsAcc()`	saveDsAcc
`setAccessibility()`	Attach a peak accessibility matrix (+ peak coordinates) to a DsASC object
`setConfigElement()`	setConfigElement
`[`(<DsATAC>,<ANY>,<ANY>,<ANY>)	Subsetting DsATAC datasets by sample
`transformCounts(<DsATAC>)`	transformCounts-methods
`unsupervisedAnalysisSc(<DsATACsc>)`	unsupervisedAnalysisSc-methods

Reference

All functions