ChromatinAssay-class: The ChromatinAssay class

ChromatinAssay-classR Documentation

The ChromatinAssay class

Description

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.


timoast/signac documentation built on Jan. 1, 2023, 7:39 a.m.