Calculate fraction of reads in peaks per cell — FRiP • Signac

Calculate fraction of reads in peaks per cell

FRiP(object, assay, total.fragments, col.name = "FRiP", verbose = TRUE)

Arguments

object: A Seurat object
assay: Name of the assay containing a peak x cell matrix
total.fragments: Name of a metadata column containing the total number of sequenced fragments for each cell. This can be computed using the CountFragments function.
col.name: Name of column in metadata to store the FRiP information.
verbose: Display messages

Value

Returns a Seurat object

Examples

FRiP(object = atac_small, assay = 'peaks', total.fragments = "fragments")
#> Calculating fraction of reads in peaks per cell
#> 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