Calculate fraction of reads in peaks per cell

Source: R/preprocessing.R

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 other assays present: bins, RNA
#>  2 dimensional reductions calculated: lsi, umap