Modeling for Single-Cell Open Chromatin Analysis
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Documentation for package ‘MOCHA’ version 1.1.0
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 |
| exportCoverage | 'exportCoverage' |
| exportDifferentials | 'exportDifferentials' |
| exportMotifs | 'exportMotifs' |
| exportOpenTiles | 'exportOpenTiles' |
| exportSmoothedInsertions | 'exportSmoothedInsertions' |
| extractRegion | 'extractRegion' |
| filterCoAccessibleLinks | 'filterCoAccessibleLinks' |
| finalModelObject | finalModelObject |
| getAltTSS | Annotate Peaks falling in Transcription Start Sites (TSS) and identify alternatively regulated TSSs for each gene. |
| getAnnotationDbFromInstalledPkgname | 'getAnnotationDbFromInstalledPkgname' Loads and attaches an installed TxDb or OrgDb-class Annotation database package. |
| getCellPopMatrix | 'getCellPopMatrix' |
| getCellTypes | 'getCellTypes' Extract cell type names from a Tile Results or Sample Tile object. |
| getCellTypeTiles | 'getCellTypeTiles' Extract the GRanges for a particular cell type |
| getCoAccessibleLinks | 'getCoAccessibleLinks' |
| getCoverage | Get sample-specific coverage files for each sample-cell population. |
| getDifferentialAccessibleTiles | 'getDifferentialAccessibleTiles' |
| getIntensityThreshold | 'getIntensityThreshold' |
| getModelValues | getModelValues from runZIGLMM output. |
| getPopFrags | Extract fragments by populations from an ArchR Project |
| getPromoterGenes | 'getPromoterGenes' |
| getSampleCellTypeMetadata | 'getSampleCellTypeMetadata' Extract Sample-celltype specific metadata |
| getSampleTileMatrix | 'getSampleTileMatrix' |
| getSequencingBias | 'getSequencingBias' |
| GRangesToString | 'GRangesToString' Converts a GRanges object to a string in the format 'chr1:100-200' |
| mergeTileResults | 'mergeTileResults' |
| MotifEnrichment | 'MotifEnrichment' |
| MotifSetEnrichmentAnalysis | 'MotifSetEnrichmentAnalysis' |
| packMOCHA | 'packMOCHA' |
| 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' |
| plotIntensityDistribution | 'plotIntensityDistribution' |
| plotRegion | 'plotRegion' |
| renameCellTypes | 'renameCellTypes' |
| 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 | 'subsetMOCHAObject' |
| testCoAccessibility | 'testCoAccessibility' |
| unpackMOCHA | 'unpackMOCHA' |
| varZIGLMM | Zero-inflated Variance Decomposition for pseudobulked scATAC data |
| youden_threshold | youden_threshold |