RegionMatrix function

Region enrichment analysis

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

Returns

Returns a Seurat object