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,
  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

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
atac_small <- SetFragments(object = atac_small, file = fpath)
NucleosomeSignal(object = atac_small)
#> Extracting reads in requested region
#> Computing ratio of mononucleosomal to nucleosome-free fragments
#> An object of class Seurat 
#> 300 features across 100 samples within 3 assays 
#> Active assay: peaks (100 features, 90 variable features)
#>  2 other assays present: bins, RNA
#>  2 dimensional reductions calculated: lsi, umap