Calculate fraction of reads in peaks per cell

Source: R/preprocessing.R

Calculate fraction of reads in peaks per cell

FRiP(object, peak.assay, bin.assay, chromosome = "chr1", verbose = TRUE)

Arguments

object

A Seurat object
peak.assay

Name of the assay containing a peak x cell matrix
bin.assay

Name of the assay containing a bin x cell matrix
chromosome

Which chromosome to use. Default is chromosome 1 ('chr1'). If NULL, use the whole genome.
verbose

Display messages

Value

Returns a Seurat object

Examples

FRiP(object = atac_small, peak.assay = 'peaks', bin.assay = 'bins')
#> Calculating fraction of reads in peaks per cell
#> 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