RegionMatrix: Region enrichment analysis

In Signac: Analysis of Single-Cell Chromatin Data

Region enrichment analysis

Description

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

Usage

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

Signac documentation built on Sept. 11, 2024, 9:30 p.m.