Signac: NucleosomeSignal – R documentation

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NucleosomeSignal

Description

Calculate the strength of the nucleosome signal per cell. Computes the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free)

Usage

NucleosomeSignal(
  object,
  assay = NULL,
  n = ncol(object) * 5000,
  verbose = TRUE,
  ...
)

Arguments

`object`	A Seurat object
`assay`	Name of assay to use. Only required if a fragment path is not provided. If NULL, use the active assay.
`n`	Number of lines to read from the fragment file. If NULL, read all lines. Default scales with the number of cells in the object.
`verbose`	Display messages
`...`	Arguments passed to other functions

Value

Returns a Seurat object with added metadata for the ratio of mononucleosomal to nucleosome-free fragments per cell, and the percentile rank of each ratio.

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
Fragments(atac_small) <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  tolerance = 0.5
)
NucleosomeSignal(object = atac_small)

Signac

Analysis of Single-Cell Chromatin Data

v1.2.1

MIT + file LICENSE

Authors

Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)

Initial release

2021-05-11