The ChromatinAssay class

The ChromatinAssay object is an extended Assay for the storage and analysis of single-cell chromatin data.

Slots

ranges

A GRanges object describing the genomic location of features in the object

motifs

A Motif object

fragments

A list of Fragment objects.

seqinfo

A Seqinfo object containing basic information about the genome sequence used.

annotation

A 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)

positionEnrichment

A named list of matrices containing positional enrichment scores for Tn5 integration (for example, enrichment at the TSS)

links

A GRanges object describing linked genomic positions, such as co-accessible sites or enhancer-gene regulatory relationships. This should be a GRanges object, where the start and end coordinates are the two linked genomic positions, and must contain a "score" metadata column.