Signac (version 0.2.4)

NucleosomeSignal: 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,
  region = "chr1-1-249250621",
  min.threshold = 147,
  max.threshold = 294,
  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.

region

Which region to use. Can be a GRanges region, a string, or a vector of strings. Default is human chromosome 1.

min.threshold

Lower bound for the mononucleosome size. Default is 147

max.threshold

Upper bound for the mononucleosome size. Default is 294

verbose

Display messages

...

Additional arguments passed to GetReadsInRegion

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

# NOT RUN {
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
atac_small <- SetFragments(object = atac_small, file = fpath)
NucleosomeSignal(object = atac_small)
# }

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