Create a RegionAggregation object — CreateRegionAggregationObject • Signac

Create a RegionAggregation-class() object to store the insertions over group of regions

Usage

CreateRegionAggregationObject(
  mat,
  regions,
  upstream,
  downstream,
  name,
  cells = NULL,
  expected = NULL,
  verbose = TRUE
)

mat: A cell-by-position matrix
regions: A GenomicRanges::granges() object containing the regions aggregated across.
upstream: Integer denoting number of bases upstream of the centered position that are stored in the matrix
downstream: Integer denoting number of bases downstream of the centered position that are stored in the matrix
name: A name for the set of regions aggregated
cells: A vector of cells where each element is the cell barcode included in the region aggregation matrix. The order of cells in this vector should correspond to the order of cells in the matrix. If NULL, cell names will be extracted from the rownames of the matrix.
expected: A vector containing expected number of Tn5 insertions per position. If NULL, the expected value will be set uniformly to 1 for each position.
verbose: Display messages.