ChromatinAssay-class function

The ChromatinAssay class

The ChromatinAssay object is an extended Assay

for the storage and analysis of single-cell chromatin data. class

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.