RegionAggregation class

The RegionAggregation class enables storage of counts centered on a group of genomic regions, aggregated across regions for each cell. The main data object stored is a cell-by-position matrix.

Usage

# S3 method for class 'RegionAggregation'
subset(x, cells = NULL, ...)

Arguments

x

A RegionAggregation object

cells

Vector of cells to retain

...

Arguments passed to other methods

Slots

matrix

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

expected

A vector containing expected number of Tn5 insertions per position

cells

A vector of cell barcodes present in the region aggregation matrix. Each entry in the cells vector corresponds to a row in the region aggregation matrix.