Region enrichment analysis

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

RegionMatrix(object, ...)

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

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

# S3 method for default
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