Region enrichment analysis — RegionMatrix • Signac

Count fragments within a set of regions for different groups of cells.

RegionMatrix(object, ...)

# S3 method for class 'Seurat'
RegionMatrix(
  object,
  regions,
  key,
  assay = NULL,
  group.by = NULL,
  idents = NULL,
  upstream = 3000,
  downstream = 3000,
  verbose = TRUE,
  ...
)

# S3 method for class 'ChromatinAssay'
RegionMatrix(
  object,
  regions,
  key,
  assay = NULL,
  group.by = NULL,
  idents = NULL,
  upstream = 3000,
  downstream = 3000,
  verbose = TRUE,
  ...
)

# Default S3 method
RegionMatrix(
  object,
  regions,
  key,
  assay = NULL,
  group.by = NULL,
  idents = NULL,
  upstream = 3000,
  downstream = 3000,
  verbose = TRUE,
  ...
)

Arguments

object: A Seurat or ChromatinAssay object
...: Arguments passed to other methods
regions: A GRanges object containing the set of genomic ranges to quantify
key: Name to store resulting matrices under
assay: Name of assay to use. If NULL, use the default assay
group.by: Grouping variable to use when aggregating data across cells. If NULL, use the active cell identities
idents: Cell identities to include. If NULL, include all identities
upstream: Number of bases to extend regions upstream
downstream: Number of bases to extend regions downstream
verbose: Display messages

Value

Returns a Seurat object