Function reference • Signac

Object interaction Functions for interacting with a Signac classes
`Annotation()` `Annotation<-`()	Annotation
`Cells<-`()	Set and get cell barcode information for a Fragment object
`ChromatinAssay-class` `ChromatinAssay`	The ChromatinAssay class
`CreateChromatinAssay()`	Create ChromatinAssay object
`Fragments()` `Fragments<-`()	Get the Fragment objects
`GetFragmentData()`	Get Fragment object data
`Links()` `Links<-`()	Get or set links information
`Motifs()` `Motifs<-`()	Get or set a motif information
`Signac` `Signac-package`	Signac: Analysis of Single-Cell Chromatin Data
`as.ChromatinAssay()`	Convert objects to a ChromatinAssay
Quantification and peak calling Functions for identifying and quantifying genomic regions
`AggregateTiles()`	Quantify aggregated genome tiles
`CallPeaks()`	Call peaks
`FeatureMatrix()`	Feature Matrix
`GenomeBinMatrix()`	Genome bin matrix
Preprocessing Functions for preprocessing single-cell data
`BinarizeCounts()`	Binarize counts
`CreateMotifMatrix()`	Create motif matrix
`DownsampleFeatures()`	Downsample Features
`FindTopFeatures()`	Find most frequently observed features
`RunTFIDF()`	Compute the term-frequency inverse-document-frequency
`UnifyPeaks()`	Unify genomic ranges
Quality control Functions for performing quality control
`FRiP()`	Calculate fraction of reads in peaks per cell
`FragmentHistogram()`	Plot fragment length histogram
`NucleosomeSignal()`	NucleosomeSignal
`TSSEnrichment()`	Compute TSS enrichment score per cell
`TSSPlot()`	Plot signal enrichment around TSSs
Dimension reduction Functions for reducing dimensions
`Jaccard()`	Calculate the Jaccard index between two matrices
`RunSVD()`	Run singular value decomposition
Visualization Functions for visualizing single-cell data
`AnnotationPlot()`	Plot gene annotations
`BigwigTrack()`	Plot data from BigWig files
`CombineTracks()`	Combine genome region plots
`CoverageBrowser()`	Genome browser
`CoveragePlot()`	Plot Tn5 insertion frequency over a region
`DensityScatter()`	Scatterplot colored by point density
`DepthCor()`	Plot sequencing depth correlation
`ExpressionPlot()`	Plot gene expression
`FragmentHistogram()`	Plot fragment length histogram
`LinkPlot()`	Plot linked genomic elements
`MotifPlot()`	Plot DNA sequence motif
`PeakPlot()`	Plot peaks in a genomic region
`PlotFootprint()`	Plot motif footprinting results
`RegionHeatmap()`	Region heatmap
`RegionPlot()`	Region plot
`TSSPlot()`	Plot signal enrichment around TSSs
`TilePlot()`	Plot integration sites per cell
`VariantPlot()`	Plot strand concordance vs. VMR
`theme_browser()`	Genome browser theme
Utilities Utility functions for working with single-cell data
`AccessiblePeaks()`	Accessible peaks
`AddChromatinModule()`	Add chromatin module
`AverageCounts()`	Average Counts
`CellsPerGroup()`	Cells per group
`ClosestFeature()`	Closest Feature
`CountsInRegion()`	Counts in region
`Extend()`	Extend
`FractionCountsInRegion()`	Fraction of counts in a genomic region
`GRangesToString()`	GRanges to String
`GeneActivity()`	Create gene activity matrix
`GetCellsInRegion()`	Get cells in a region
`GetGRangesFromEnsDb()`	Extract genomic ranges from EnsDb object
`GetIntersectingFeatures()`	Find intersecting regions between two objects
`GetTSSPositions()`	Find transcriptional start sites
`IntersectMatrix()`	Intersect genomic coordinates with matrix rows
`LookupGeneCoords()`	Get gene coordinates
`MatchRegionStats()`	Match DNA sequence characteristics
`SortIdents()`	Sorts cell metadata variable by similarity using hierarchical clustering
`StringToGRanges()`	String to GRanges
`SubsetMatrix()`	Subset matrix rows and columns
`UnifyPeaks()`	Unify genomic ranges
Footprinting Functions for performing TF footprinting
`Footprint()`	Transcription factor footprinting analysis
`GetFootprintData()`	Get footprinting data
`InsertionBias()`	Compute Tn5 insertion bias
`PlotFootprint()`	Plot motif footprinting results
Motif analysis Functions for performing DNA sequence motif analysis
`AddMotifs()`	Add DNA sequence motif information
`ConvertMotifID()`	Convert between motif name and motif ID
`CreateMotifMatrix()`	Create motif matrix
`CreateMotifObject()`	Create motif object
`FindMotifs()`	FindMotifs
`GetMotifData()`	Retrieve a motif matrix
`MatchRegionStats()`	Match DNA sequence characteristics
`Motif-class` `Motif`	The Motif class
`MotifCounts()`	Count fragments surrounding motif sites
`MotifPlot()`	Plot DNA sequence motif
`Motifs()` `Motifs<-`()	Get or set a motif information
`RegionStats()`	Compute base composition information for genomic ranges
`RunChromVAR()`	Run chromVAR
`SetMotifData()`	Set motif data
`subset(<Motif>)` `[`(<Motif>)	Subset a Motif object
Heatmaps Functions for single-cell heatmaps
`RegionHeatmap()`	Region heatmap
`RegionMatrix()`	Region enrichment analysis
`RegionPlot()`	Region plot
Mitochondrial lineage tracing Functions for identifying cell lineages or clonotypes from mitochondrial mutations
`AlleleFreq()`	Compute allele frequencies per cell
`ClusterClonotypes()`	Find relationships between clonotypes
`FindClonotypes()`	Find clonotypes
`IdentifyVariants()`	Identify mitochondrial variants
`ReadMGATK()`	Read MGATK output
`VariantPlot()`	Plot strand concordance vs. VMR
Fragments Functions for working with fragment files
`Cells(<Fragment>)` `Cells<-`(<Fragment>)	Set and get cell barcode information for a `Fragment` object
`CountFragments()`	Count fragments
`CreateFragmentObject()`	Create a Fragment object
`FilterCells()`	Filter cells from fragment file
`Fragment-class` `Fragment`	The Fragment class
`Fragments()` `Fragments<-`()	Get the Fragment objects
`SplitFragments()`	Split fragment file by cell identities
`UpdatePath()`	Update the file path for a Fragment object
`ValidateCells()`	Validate cells present in fragment file
`ValidateFragments()`	Validate Fragment object
`ValidateHash()`	Validate hashes for Fragment object
`head(<Fragment>)`	Return the first rows of a fragment file
`subset(<Fragment>)`	Subset a Fragment object
Links Functions for working with genomic links
`ConnectionsToLinks()`	Cicero connections to links
`GetLinkedGenes()`	Get genes linked to peaks
`GetLinkedPeaks()`	Get peaks linked to genes
`LinkPeaks()`	Link peaks to genes
`LinkPlot()`	Plot linked genomic elements
`Links()` `Links<-`()	Get or set links information
Nearest methods Nearest genomic range methods for Signac-defined classes
`precede(<ANY>,<ChromatinAssay>)` `precede(<ChromatinAssay>,<ANY>)` `precede(<ChromatinAssay>,<ChromatinAssay>)` `precede(<ANY>,<Seurat>)` `precede(<Seurat>,<ANY>)` `precede(<Seurat>,<Seurat>)` `follow(<ANY>,<ChromatinAssay>)` `follow(<ChromatinAssay>,<ANY>)` `follow(<ChromatinAssay>,<ChromatinAssay>)` `follow(<ANY>,<Seurat>)` `follow(<Seurat>,<ANY>)` `follow(<Seurat>,<Seurat>)` `nearest(<ANY>,<ChromatinAssay>)` `nearest(<ChromatinAssay>,<ANY>)` `nearest(<ChromatinAssay>,<ChromatinAssay>)` `nearest(<ANY>,<Seurat>)` `nearest(<Seurat>,<ANY>)` `nearest(<Seurat>,<Seurat>)` `distance(<ANY>,<ChromatinAssay>)` `distance(<ChromatinAssay>,<ANY>)` `distance(<ChromatinAssay>,<ChromatinAssay>)` `distance(<ANY>,<Seurat>)` `distance(<Seurat>,<ANY>)` `distance(<Seurat>,<Seurat>)` `distanceToNearest(<ANY>,<ChromatinAssay>)` `distanceToNearest(<ChromatinAssay>,<ANY>)` `distanceToNearest(<ChromatinAssay>,<ChromatinAssay>)` `distanceToNearest(<ANY>,<Seurat>)` `distanceToNearest(<Seurat>,<ANY>)` `distanceToNearest(<Seurat>,<Seurat>)`	Find the nearest range neighbors for ChromatinAssay objects
Inter-range methods Inter-range methods for Signac-defined classes
`range(<ChromatinAssay>)` `range(<Seurat>)` `reduce(<ChromatinAssay>)` `reduce(<Seurat>)` `gaps(<ChromatinAssay>)` `gaps(<Seurat>)` `disjoin(<ChromatinAssay>)` `disjoin(<Seurat>)` `isDisjoint(<ChromatinAssay>)` `isDisjoint(<Seurat>)` `disjointBins(<ChromatinAssay>)` `disjointBins(<Seurat>)`	Inter-range transformations for ChromatinAssay objects
Overlap methods Overlap-range methods for Signac-defined classes
`findOverlaps(<Vector>,<ChromatinAssay>)` `findOverlaps(<ChromatinAssay>,<Vector>)` `findOverlaps(<ChromatinAssay>,<ChromatinAssay>)` `findOverlaps(<Vector>,<Seurat>)` `findOverlaps(<Seurat>,<Vector>)` `findOverlaps(<Seurat>,<Seurat>)` `countOverlaps(<Vector>,<ChromatinAssay>)` `countOverlaps(<ChromatinAssay>,<Vector>)` `countOverlaps(<ChromatinAssay>,<ChromatinAssay>)` `countOverlaps(<Seurat>,<Vector>)` `countOverlaps(<Vector>,<Seurat>)` `countOverlaps(<Seurat>,<Seurat>)`	Find overlapping ranges for ChromatinAssay objects
Coverage methods Genomic range coverage methods for Signac-defined classes
`coverage(<ChromatinAssay>)` `coverage(<Seurat>)`	Coverage of a ChromatinAssay object
Genomic range methods Genomic ranges methods for Signac-defined classes
`granges(<ChromatinAssay>)` `granges(<Seurat>)`	Access genomic ranges for ChromatinAssay objects
Seqinfo methods Seqinfo methods for Signac-defined classes
`seqinfo(<ChromatinAssay>)` `seqinfo<-`(<ChromatinAssay>) `seqlevels(<ChromatinAssay>)` `seqlevels<-`(<ChromatinAssay>) `seqnames(<ChromatinAssay>)` `seqnames<-`(<ChromatinAssay>) `seqlengths(<ChromatinAssay>)` `seqlengths<-`(<ChromatinAssay>) `genome(<ChromatinAssay>)` `genome<-`(<ChromatinAssay>) `isCircular(<ChromatinAssay>)` `isCircular<-`(<ChromatinAssay>) `seqinfo(<Seurat>)` `seqinfo<-`(<Seurat>) `seqlevels(<Seurat>)` `seqlevels<-`(<Seurat>) `seqnames(<Seurat>)` `seqnames<-`(<Seurat>) `seqlengths(<Seurat>)` `seqlengths<-`(<Seurat>) `genome(<Seurat>)` `genome<-`(<Seurat>) `isCircular(<Seurat>)` `isCircular<-`(<Seurat>)	Access and modify sequence information for ChromatinAssay objects
Data Datasets included in Signac
`atac_small`	A small example scATAC-seq dataset
`blacklist_ce10`	Genomic blacklist regions for C. elegans ce10 (0-based)
`blacklist_ce11`	Genomic blacklist regions for C. elegans ce11 (0-based)
`blacklist_dm3`	Genomic blacklist regions for Drosophila dm3 (0-based)
`blacklist_dm6`	Genomic blacklist regions for Drosophila dm6 (0-based)
`blacklist_hg19`	Genomic blacklist regions for Human hg19 (0-based)
`blacklist_hg38`	Genomic blacklist regions for Human GRCh38
`blacklist_hg38_unified`	Unified genomic blacklist regions for Human GRCh38
`blacklist_mm10`	Genomic blacklist regions for Mouse mm10 (0-based)

Reference

Object interaction

Quantification and peak calling

Preprocessing

Quality control

Dimension reduction

Visualization

Utilities

Footprinting

Motif analysis

Heatmaps

Mitochondrial lineage tracing

Fragments

Links

Nearest methods

Inter-range methods

Overlap methods

Coverage methods

Genomic range methods

Seqinfo methods

Data