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

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
)
#> Computing hash
NucleosomeSignal(object = atac_small)
#> An object of class Seurat 
#> 1323 features across 100 samples within 3 assays 
#> Active assay: peaks (323 features, 323 variable features)
#>  2 other assays present: bins, RNA
#>  2 dimensional reductions calculated: lsi, umap