NucleosomeSignal function

NucleosomeSignal

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)

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

Returns

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)