Fragments: Get the Fragment objects

In timoast/signac: Analysis of Single-Cell Chromatin Data

Get the Fragment objects

Description

Get the Fragment objects

Usage

Fragments(object, ...)

Fragments(object, ...) <- value

## S3 method for class 'ChromatinAssay'
Fragments(object, ...)

## S3 method for class 'Seurat'
Fragments(object, ...)

## S3 replacement method for class 'ChromatinAssay'
Fragments(object, ...) <- value

## S3 replacement method for class 'Seurat'
Fragments(object, ...) <- value

Arguments

object	A Seurat object or ChromatinAssay object
...	Arguments passed to other methods
value	A Fragment object or list of Fragment objects

Value

Returns a list of Fragment objects. If there are no Fragment objects present, returns an empty list.

Examples

Fragments(atac_small[["peaks"]])
Fragments(atac_small)
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  validate.fragments = FALSE
)
Fragments(atac_small[["bins"]]) <- fragments
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  validate.fragments = FALSE
)
Fragments(atac_small) <- fragments

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.