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,
...
)A Seurat object
Name of assay to use. Only required if a fragment path is not provided. If NULL, use the active assay.
Number of lines to read from the fragment file. If NULL, read all lines. Default scales with the number of cells in the object.
Display messages
Arguments passed to other functions
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.
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 layers present: counts, data
#> 2 other assays present: bins, RNA
#> 2 dimensional reductions calculated: lsi, umap