# Modeling for Single-Cell Open Chromatin Analysis

## Documentation for package ‘MOCHA’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.callOpenTiles_ArchR | 'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project.
.counts_plot_default_theme | Default ggplot theme for counts plot
.gene_plot_theme | Common theme for gene plots
addAccessibilityShift | 'addAccessibilityShift'
addMotifSet | 'addMotifSet'
annotateTiles | 'annotateTiles'
bulkDimReduction | 'bulkDimReduction'
bulkUMAP | 'bulkUMAP'
callOpenTiles | 'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project.
callOpenTiles-method | 'callOpenTiles' Perform peak-calling on a set of fragments or an ArchR Project.
combineSampleTileMatrix | 'combineSampleTileMatrix'
differentialsToGRanges | 'differentialsToGRanges' Converts a data.frame matrix to a GRanges, preserving additional columns as GRanges metadata
exampleBlackList | exampleBlackList
exampleCellColData | exampleCellColData
exampleFragments | exampleFragments
extractRegion | 'extractRegion'
filterCoAccessibleLinks | 'filterCoAccessibleLinks'
finalModelObject | finalModelObject
getAltTSS | Annotate Peaks falling in Transcription Start Sites (TSS) and identify alternatively regulated TSSs for each gene.
getCellPopMatrix | 'getCellPopMatrix'
getCoAccessibleLinks | 'getCoAccessibleLinks'
getCoverage | Get sample-specific coverage files for each sample-cell population.
getDifferentialAccessibleTiles | 'getDifferentialAccessibleTiles'
getModelValues | getModelValues from runZIGLMM output.
getPopFrags | Extract fragments by populations from an ArchR Project
getSampleTileMatrix | 'getSampleTileMatrix'
GRangesToString | 'GRangesToString' Converts a GRanges object to a string in the format 'chr1:100-200'
MotifEnrichment | 'MotifEnrichment'
MotifSetEnrichmentAnalysis | 'MotifSetEnrichmentAnalysis'
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
plotConsensus | 'plotConsensus'
plotRegion | 'plotRegion'
runLMEM | Run Linear Mixed-Effects Modeling for continuous, non-zero inflated data
runZIGLMM | Run Zero-inflated Generalized Linear Mixed Modeling on pseudobulked scATAC data
StringsToGRanges | 'StringsToGRanges'
subsetMOCHAObject | 'subsetObject'
testCoAccessibility | 'testCoAccessibility'
youden_threshold | youden_threshold