Convert objects to a ChromatinAssay

Source: R/generics.R, R/objects.R

Convert objects to a ChromatinAssay

as.ChromatinAssay(x, ...)

# S3 method for class 'Assay'
as.ChromatinAssay(
  x,
  ranges = NULL,
  seqinfo = NULL,
  annotation = NULL,
  motifs = NULL,
  fragments = NULL,
  bias = NULL,
  positionEnrichment = NULL,
  sep = c("-", "-"),
  ...
)

Arguments

x

An object to convert to class ChromatinAssay

...

Arguments passed to other methods

ranges

A GRanges object

seqinfo

A Seqinfo object containing basic information about the genome used. Alternatively, the name of a UCSC genome can be provided and the sequence information will be downloaded from UCSC.

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")

motifs

A Motif object

fragments

A list of Fragment objects

bias

Tn5 integration bias matrix

positionEnrichment

A named list of position enrichment matrices.

sep

Characters used to separate the chromosome, start, and end coordinates in the row names of the data matrix