# Analyzing single-cell regulatory chromatin in R.

## Documentation for package ‘ArchR’ version 1.0.3

- DESCRIPTION file.

## Help Pages

A C E F G I L M N P R S T V misc

## -- A --

addArchRAnnotations | Add ArchR annotations to an ArchRProject
addArchRChrPrefix | Add a globally-applied requirement for chromosome prefix
addArchRDebugging | Set ArchR Debugging
addArchRGenome | Add a globally defined genome to all ArchR functions.
addArchRH5Level | Add a globally-applied compression level for h5 files
addArchRLocking | Add a globally-applied H5 file locking setup
addArchRLogging | Set ArchR Logging
addArchRThreads | Add a globally-applied number of threads to use for parallel computing.
addArchRVerbose | Set ArchR Verbosity for Log Messaging
addBgdPeaks | Add Background Peaks to an ArchRProject
addCellColData | Add information to cellColData in an ArchRProject
addClusters | Add cluster information to an ArchRProject
addCoAccessibility | Add Peak Co-Accessibility to an ArchRProject
addCombinedDims | Combine two or more modalities dimensionality reductions.
addDemuxletResults | Add Demuxlet Results to ArchR Project
addDeviationsMatrix | Add a matrix of deviations for a given peakAnnotation to Arrow Files in ArchRProject
addDoubletScores | Add Doublet Scores to a collection of ArrowFiles or an ArchRProject
addFeatureCounts | This function will add total counts of scATAC cells in provided features into ArchRProject.
addFeatureMatrix | Add a feature matrix to an ArchRProject or a set of ArrowFiles
addGeneExpressionMatrix | Add Gene Expression Matrix to ArrowFiles or an ArchRProject
addGeneIntegrationMatrix | Add a GeneIntegrationMatrix to ArrowFiles or an ArchRProject
addGeneScoreMatrix | Add GeneScoreMatrix to ArrowFiles or an ArchRProject
addGroupCoverages | Add Group Coverages to an ArchRProject object
addHarmony | Add Harmony Batch Corrected Reduced Dims to an ArchRProject
addImputeWeights | Add Imputation Weights to an ArchRProject
addIterativeLSI | Add an Iterative LSI-based dimensionality reduction to an ArchRProject
addModuleScore | Add Module Scores to an ArchRProject
addMonocleTrajectory | Add a Monocle Trajectory to an ArchR Project
addMotifAnnotations | Add motif annotations to an ArchRProject
addPeak2GeneLinks | Add Peak2GeneLinks to an ArchRProject
addPeakAnnotations | Add peak annotations to an ArchRProject
addPeakMatrix | Add a Peak Matrix to the ArrowFiles of an ArchRProject
addPeakSet | Add a peak set to an ArchRProject
addProjectSummary | Add projectSummary to an ArchRProject
addReproduciblePeakSet | Add a Reproducible Peak Set to an ArchRProject
addSampleColData | Add information to sampleColData in an ArchRProject
addSlingShotTrajectories | Add a Slingshot Trajectories to an ArchR Project
addTileMatrix | Add TileMatrix to ArrowFiles or an ArchRProject
addTrajectory | Add a Supervised Trajectory to an ArchR Project
addTSNE | Add a TSNE embedding of a reduced dimensions object to an ArchRProject
addUMAP | Add a UMAP embedding of a reduced dimensions object to an ArchRProject
ArchRBrowser | Launch ArchR Genome Browser
ArchRHeatmap | Plot Nice Lookng Heatmap Using Complex Heatmap
ArchRPalettes | List of color palettes that can be used in plots
ArchRProject | Create ArchRProject from ArrowFiles

## -- C --

confusionMatrix | Create a Confusion Matrix based on two value vectors
correlateMatrices | Correlate Matrices within an ArchRProject
correlateTrajectories | Correlate Trajectories
createArrowFiles | Create Arrow Files
createGeneAnnotation | Create a gene annotation object for ArchR
createGenomeAnnotation | Create a genome annotation object for ArchR
createLogFile | Create a Log File for ArchR
customEnrichment | Hypergeometric Enrichment in input peak ranges.

## -- E --

exportPeakMatrixForSTREAM | Get a PeakMatrix stored in an ArchRProject and write out for STREAM
extendGR | Extend regions from a Genomic Ranges object

## -- F --

filterChrGR | Filters unwanted seqlevels from a Genomic Ranges object or similar object
filterDoublets | Filter Doublets From an ArchRProject
findMacs2 | Find the installed location of the MACS2 executable

## -- G --

getArchRChrPrefix | Get a globally-applied requirement for chromosome prefix
getArchRDebugging | Get ArchR Debugging
getArchRGenome | Get the globally defined genome, the geneAnnotation, or genomeAnnotation objects associated with the globally defined genome.
getArchRH5Level | Get globally-applied compression level for h5 files
getArchRLogging | Get ArchR Logging
getArchRThreads | Get globally-applied number of threads to use for parallel computing.
getArchRVerbose | Set ArchR Verbosity for Log Messaging
getArrowFiles | Get ArrowFiles from an ArchRProject
getAvailableMatrices | Get a list available matrices in the ArrowFiles storted in an ArchRProject
getBgdPeaks | Get Background Peaks from an ArchRProject
getBlacklist | Get the blacklist from an ArchRProject
getCellColData | Get cellColData from an ArchRProject
getCellNames | Get cellNames from an ArchRProject
getChromLengths | Get chromLengths from ArchRProject
getChromSizes | Get chromSizes from ArchRProject
getCoAccessibility | Get the peak co-accessibility from an ArchRProject
getEmbedding | Get embedding information stored in an ArchRProject
getExons | Get the exons from an ArchRProject
getFeatures | Get the features that could be selected from a given data matrix within an ArchRProject
getFootprints | Calculate footprints from an ArchRProject
getFragmentsFromArrow | Get the fragments from an ArrowFile
getFragmentsFromProject | Get the fragments from an ArchRProject
getGeneAnnotation | Get geneAnnotation from an ArchRProject
getGenes | Get the genes from an ArchRProject
getGenome | Get the genome used by an ArchRProject
getGenomeAnnotation | Get the genomeAnnotation from an ArchRProject
getGroupBW | Export Group BigWigs
getGroupFragments | Export Group Fragment Files
getGroupSE | Export Group Summarized Experiment
getGroupSummary | Get summary for Groups in ArchRProject
getImputeWeights | Get Imputation Weights from ArchRProject
getInputFiles | Get Input Files from paths to create arrows
getMarkerFeatures | Identify Marker Features for each cell grouping
getMarkers | Get Marker Features from a marker summarized experiment
getMatches | Get peak annotation matches from an ArchRProject
getMatrixFromArrow | Get a data matrix stored in an ArrowFile
getMatrixFromProject | Get a data matrix stored in an ArchRProject
getMonocleTrajectories | Get a Monocle CDS of Trajectories that can be added to an ArchRProject
getOutputDirectory | Get outputDirectory from an ArchRProject
getPBGroupSE | Export PseudoBulk Group Summarized Experiment
getPeak2GeneLinks | Get the peak-to-gene links from an ArchRProject
getPeakAnnotation | Get peakAnnotation from an ArchRProject
getPeakSet | Get the peak set from an ArchRProject
getPositions | Get peak annotation positions from an ArchRProject
getProjectSummary | Get projectSummary from an ArchRProject
getReducedDims | Get dimensionality reduction information stored in an ArchRProject
getSampleColData | Get sampleColData from an ArchRProject
getSampleNames | Get the sample names from an ArchRProject
getSeqnames | Get the seqnames that could be selected from a given data matrix within an ArchRProject
getTestArrow | Get PBMC Small Test Arrow file
getTestFragments | Get PBMC Small Test Fragments
getTestProject | Get PBMC Small Test Project
getTrajectory | Get Supervised Trajectory from an ArchR Project
getTSS | Get the transcription start sites of all genes in an ArchRProject
getTutorialData | Get Relevant Data For ArchR Tutorials
getValidBarcodes | Get Valid Barcodes from 10x Cell Ranger output to pre-filter barcodes
getVarDeviations | Get Variable Deviations across cells in ArchRProject.
ggAlignPlots | Align ggplot plots vertically or horizontally
ggGroup | A ggplot-based ridge/violin plot wrapper function
ggHex | A ggplot-based Hexplot wrapper function summary of points in a standardized manner
ggOneToOne | A ggplot-based one-to-one dot plot wrapper function
ggPoint | A ggplot-based dot plot wrapper function

## -- I --

import10xFeatureMatrix | Import Feature Matrix from 10x Feature HDF5 file.
imputeMatrix | Impute a matrix with impute weights
installExtraPackages | Install extra packages used in ArchR that are not installed by default

## -- L --

loadArchRProject | Load Previous ArchRProject into R

## -- M --

mapLabels | Re-map a character vector of labels from an old set of labels to a new set of labels

## -- N --

nCells | Get the number of cells from an ArchRProject/ArrowFile
nonOverlappingGR | Retreive a non-overlapping set of regions from a Genomic Ranges object

## -- P --

paletteContinuous | Continuous Color Palette
paletteDiscrete | Optimized discrete color palette generation
peakAnnoEnrichment | Peak Annotation Hypergeometric Enrichment in Marker Peaks.
plotBrowserTrack | Plot an ArchR Region Track
plotEmbedding | Visualize an Embedding from ArchR Project
plotEnrichHeatmap | Plot a Heatmap of Peak Annotation Hypergeometric Enrichment in Marker Peaks.
plotFootprints | Plot Footprints
plotFragmentSizes | Plot the fragment size distribution for each sample
plotGroups | Visualize Groups from ArchR Project
plotMarkerHeatmap | Plot a Heatmap of Identified Marker Features
plotMarkers | Plot Differential Markers
plotPDF | Plot PDF in outputDirectory of an ArchRProject
plotPeak2GeneHeatmap | Plot Peak2Gene Heatmap from an ArchRProject
plotTrajectory | Visualize a Trajectory from ArchR Project
plotTrajectoryHeatmap | Plot a Heatmap of Features across a Trajectory
plotTSSEnrichment | Plot a TSS Enrichment Plot for Each Sample
projectBulkATAC | Project Bulk ATAC-seq data into single cell subspace

## -- R --

recoverArchRProject | Recover ArchRProject if broken sampleColData/cellColData
reformatFragmentFiles | Reformat Fragment Files to be Tabix and Chr Sorted

## -- S --

saveArchRProject | Save ArchRProject for Later Usage
setArchRLocking | Set a globally-applied H5 file locking setup
subsetArchRProject | Subset an ArchRProject for downstream analysis
subsetCells | Subset cells in an ArchRProject.

## -- T --

theme_ArchR | ggplot2 default theme for ArchR

## -- V --

validBSgenome | Get/Validate BSgenome

## -- misc --

$.ArchRProject | Accessing cellColData directly from dollar.sign accessor
$<-.ArchRProject | Add directly to cellColData directly from dollar.sign accessor
%bcin% | Generic matching function for S4Vector objects
%bcni% | Negated matching function for S4Vector objects
%ni% | Negated Value Matching
.DollarNames.ArchRProject | Accessing cellColData directly from dollar.sign accessor
[.ArchRProject | Subset cells directly from ArchRProject