ChromatinAssay-class: The ChromatinAssay class

Description Slots

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

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.


Signac documentation built on Dec. 11, 2021, 9:55 a.m.