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ChromatinAssay5 and GRangesAssay object constructors

Source: R/objects.R
CreateGRangesAssay.Rd

The ChromatinAssay5-class() and GRangesAssay-class() classes extend SeuratObject::Assay5() objects for single-cell chromatin data, with or without genomic ranges for each feature in the assay. Use CreateGRangesAssay to construct a GRangesAssay object or CreateChromatinAssay5 to construct a ChromatinAssay5 object.

Usage

CreateGRangesAssay(counts, data, ranges = NULL, ...)

CreateChromatinAssay5(
  counts,
  data,
  fragments = NULL,
  annotation = NULL,
  motifs = NULL,
  links = NULL,
  bias = NULL,
  region.aggregation = NULL,
  validate.fragments = TRUE,
  verbose = TRUE,
  ...
)

Arguments

counts

A two-dimensional matrix

data

Optional pre-normalized count matrix

ranges

A set of GenomicRanges::GRanges() corresponding to the rows of the input matrix. If NULL, genomic ranges will be extracted from the rownames of the input data matrix, and those rownames must be formatted as chromosome:start-end.

...

Additional arguments passed to CreateChromatinAssay5() and SeuratObject::CreateAssay5Object().

fragments

Path to a tabix-indexed fragments file for the data contained in the input matrix. If multiple fragment files are required, you can add additional Fragment() object to the assay after it is created using the CreateFragmentObject() and Fragments() functions. Alternatively, a list of Fragment() objects can be provided.

annotation

A set of GenomicRanges::GRanges() containing annotations for the genome used. It must have the following columns:

  • tx_id or transcript_id: Transcript ID

  • gene_name: Gene name

  • gene_id: Gene ID

  • gene_biotype: Gene biotype (e.g. "protein_coding", "lincRNA")

  • type: Annotation type (e.g. "exon", "gap")

motifs

A Motif object

A named list of InteractionSet::GInteractions() objects

bias

A Tn5 integration bias matrix

region.aggregation

A named list of RegionAggregation objects.

validate.fragments

Check that cells in the assay are present in the fragment file.

verbose

Display messages

Value

Returns a Seurat object

See also

CreateChromatinAssay5()