Skip to contents

ChromatinAssay5 and GRangesAssay object classes

Source: R/classes.R
GRangesAssay-class.Rd

The GRangesAssay and ChromatinAssay5 classes are extended SeuratObject::Assay5() classes for the storage and analysis of single-cell chromatin data. The GRangesAssay class requires that features in the assay are genomic ranges.

Slots

fragments

A list of Fragment() objects.

annotation

A GenomicRanges::GRanges() object containing genomic annotations. This should be a GRanges object with the following columns:

  • tx_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")

bias

A vector containing Tn5 integration bias information (frequency of Tn5 integration at different kmers). This must be a named numeric vector where the name of the element corresponds to the DNA sequence and the value represents the bias value. All DNA hexamers must be present in the vector.

region.aggregation

A list of RegionAggregation objects

motifs

A Motif object

links

A list of InteractionSet::GInteractions() objects describing linked genomic positions, such as co-accessible sites, eQTLs, Hi-C contact, or enhancer-gene regulatory relationships.

ranges

A GenomicRanges::GRanges() object describing the genomic location of features in the object

See also

SeuratObject::Assay5()