Quantifies fragment counts per cell in fixed-size genome bins across the whole genome, then removes bins with less than a desired minimum number of counts in the bin, then merges adjacent tiles into a single region.
AggregateTiles(object, ...) # S3 method for Seurat AggregateTiles( object, genome, assay = NULL, new.assay.name = "tiles", min_counts = 5, binsize = 5000, verbose = TRUE, ... ) # S3 method for ChromatinAssay AggregateTiles( object, genome, min_counts = 5, binsize = 5000, verbose = TRUE, ... ) # S3 method for default AggregateTiles( object, genome, cells = NULL, min_counts = 5, binsize = 5000, verbose = TRUE, ... )
| object | A Seurat object or ChromatinAssay object |
|---|---|
| ... | Additional arguments passed to other methods |
| genome | genome A vector of chromosome sizes for the genome. This is used to construct the genome bin coordinates. The can be obtained by calling seqlengths on a BSgenome-class object. |
| assay | Name of assay to use |
| new.assay.name | Name of new assay to create containing aggregated genome tiles |
| min_counts | Minimum number of counts for a tile to be retained prior to aggregation |
| binsize | Size of the genome bins (tiles) in base pairs |
| verbose | Display messages |
| cells | Cells to include |
When running on a Seurat object, returns the Seurat object with a new
ChromatinAssay added.
When running on a ChromatinAssay, returns a new
ChromatinAssay containing the aggregated genome tiles.
When running on a fragment file, returns a sparse region x cell matrix.