Function reference • MOCHA

Open Chromatin Identification

callOpenTiles() .callOpenTiles_default() .callOpenTiles_ArchR(): Perform peak-calling on a set of fragments or an ArchR Project

getSampleTileMatrix(): Get consensus sample-tile matrices containing the signal intensity at each tile

Plotting

plotConsensus(): Plot to determine the reproducibility threshold

plotIntensityDistribution(): Plots the distribution of sample-tile intensities for a given cell population

plotRegion(): Plot a given region summarized across all cell groupings

Downstream Analyses

MotifEnrichment(): Test for enrichment of motifs against a background

MotifSetEnrichmentAnalysis(): Test the enrichment of a given TF motif set against a motif set downstream of multiple ligands

addAccessibilityShift(): Add difference in accessibility between two conditions

bulkDimReduction(): Run PCA or LSI dimensionality reduction on tiles

bulkUMAP(): Generate UMAP from pseudobulk LSI results

filterCoAccessibleLinks(): Filter links by correlation strength

getAltTSS(): Annotate peaks falling in Transcription Start Sites (TSSs) and identify alternatively regulated TSSs for each gene

getCoAccessibleLinks(): Find co-accessible neighboring regions

getDifferentialAccessibleTiles(): Conduct a differential test between open regions of two sample groups

pilotLMEM(): Execute a pilot run of single linear model on a subset of data

pilotZIGLMM(): Execute a pilot run of model on a subset of data

runLMEM(): Run Linear Mixed-Effects Modeling for continuous, non-zero inflated data

runZIGLMM(): Run Zero-inflated Generalized Linear Mixed Modeling on pseudobulked scATAC data

testCoAccessibility(): Test if tile pairs are significantly different against a random, non-overlapping background set

testCoAccessibilityChromVar(): Test input tile pairs against a ChromVAR background

testCoAccessibilityRandom(): Test input tile pairs against a random background

varZIGLMM(): Zero-inflated Variance Decomposition for pseudobulked scATAC data

exportCoverage(): Export normalized coverage files to per-sample or sample-averaged (per cell population) BigWig files.

exportDifferentials(): Export differential peaks from getDifferentialAccessibleTiles() to BigBed format for visualization in genome browsers.

exportMotifs(): Export motif annotations from addMotifSet() to BigBed format for visualization in genome browsers.

exportOpenTiles(): Export open tiles of a given cell population to BigBed format for visualization in genome browsers.

exportSmoothedInsertions(): Export insertion counts to per-sample BigWig files after applying a rolling sum and rolling median smoothing filter.

packMOCHA(): Zip up a MOCHA object and its linked files for portability between file systems

unpackMOCHA(): Unzip a MOCHA object and its linked files created by packMOCHA() for portability between file systems

Utilities

GRangesToString(): Convert a GRanges object to a string in the format 'chr1:100-200'

StringsToGRanges(): Convert a list of strings in the format "chr1:100-200" into a GRanges

addMotifSet(): Identify motifs within a peakset

annotateTiles(): Annotate tiles with gene annotations

combineSampleTileMatrix(): Merge the TSAM from multiple cell populations into a single matrix

differentialsToGRanges(): Convert a data.frame or matrix to a GRanges

extractRegion(): Get coverage for a given region

getCellPopMatrix(): Get the SampleTileMatrix of the given cell population

getCellTypeTiles(): Extract the GRanges for a particular cell population

getCellTypes(): Extract cell population names from a Tile Results or Sample Tile object.

getCoverage(): Get sample-specific coverage files for each sample-cell population

getModelValues(): Get a data.frame of model values from the output of linear modeling

getPopFrags(): Extract fragments by populations from an ArchR Project

getPromoterGenes(): Extract the list of promoter genes from a GRanges annotated with annotateTiles()

getSampleCellTypeMetadata(): Extract Sample-celltype specific metadata

mergeTileResults(): Merge tileResults from callOpenTiles() that share cell populations into a single object containing all samples

renameCellTypes(): Modify the cell population names in a Sample-Tile Object from getSampleTileMatrix()

subsetMOCHAObject(): Subset a tileResults object by metadata