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Convert objects to a GRangesAssay object

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

Convert objects to a GRangesAssay object

Usage

as.GRangesAssay(x, ...)

# S3 method for class 'ChromatinAssay'
as.GRangesAssay(x, ...)

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

# S3 method for class 'ChromatinAssay5'
as.GRangesAssay(x, ranges = NULL, ...)

Arguments

x

An object to convert to class GRangesAssay

...

Arguments passed to other methods

annotation

A set of GenomicRanges::GRanges() containing gene annotations for the genome used. 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

Path to a tabix-indexed fragments file for the data contained in the input matrix.

bias

A Tn5 integration bias matrix vector

region.aggregation

A named list of RegionAggregation-class objects.

ranges

A GRanges object

motifs

A Motif-class object

A named list of InteractionSet::GInteractions() objects