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Convert objects to a ChromatinAssay5 object

Source: R/generics.R, R/objects.R
as.ChromatinAssay5.Rd

Convert objects to a ChromatinAssay5 object

Usage

as.ChromatinAssay5(x, ...)

# S3 method for class 'Assay5'
as.ChromatinAssay5(
  x,
  annotation = NULL,
  fragments = NULL,
  bias = NULL,
  motifs = NULL,
  links = NULL,
  region.aggregation = NULL,
  ...
)

Arguments

x

An object to convert to class ChromatinAssay5

...

Arguments passed to other methods

annotation

Genomic annotation. It must have the following columns:

  • tx_id or transcript_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")

fragments

A list of Fragment2 objects

bias

Tn5 integration bias matrix

motifs

A Motif object

Genomic links TODO

region.aggregation

A named list of RegionAggregation