Quantify aggregated genome tiles
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 class 'Seurat' AggregateTiles( object, genome, assay = NULL, new.assay.name = "tiles", min_counts = 5, binsize = 5000, verbose = TRUE, ... ) ## S3 method for class 'ChromatinAssay' AggregateTiles( object, genome, min_counts = 5, binsize = 5000, verbose = TRUE, ... ) ## Default S3 method: 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.
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