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, ... )
A Seurat object or ChromatinAssay object
Additional arguments passed to other methods
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.
Name of assay to use
Name of new assay to create containing aggregated genome tiles
Minimum number of counts for a tile to be retained prior to aggregation
Size of the genome bins (tiles) in base pairs
Cells to include
When running on a Seurat object, returns the Seurat object with a new
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.