Quantify aggregated genome tiles — AggregateTiles • Signac

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.

Usage

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 'ChromatinAssay5'
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,
  ...
)

Arguments

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

Value

When running on a Seurat object, returns the Seurat object with a new ChromatinAssay5 assay added.

When running on a ChromatinAssay5, returns a new ChromatinAssay5 containing the aggregated genome tiles.

When running on a fragment file, returns a sparse region x cell matrix.