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,
...
)
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.
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
Display messages
Cells to include