Binarize counts

Set counts >1 to 1 in a count matrix

BinarizeCounts(object, ...)

# S3 method for default
BinarizeCounts(object, assay = NULL, verbose = TRUE, ...)

# S3 method for Assay
BinarizeCounts(object, assay = NULL, verbose = TRUE, ...)

# S3 method for Seurat
BinarizeCounts(object, assay = NULL, verbose = TRUE, ...)

Arguments

object	A Seurat object
...	Arguments passed to other methods
assay	Name of assay to use. Can be a list of assays, and binarization will be applied to each.
verbose	Display messages

Value

Returns a Seurat object

Examples

x <- matrix(data = sample(0:3, size = 25, replace = TRUE), ncol = 5)
BinarizeCounts(x)
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    0    1    1    1    1
#> [2,]    1    1    0    1    1
#> [3,]    1    1    0    0    1
#> [4,]    1    1    0    1    1
#> [5,]    0    1    1    1    0
BinarizeCounts(atac_small[['peaks']])
#> Assay data with 100 features for 100 cells
#> Top 10 variable features:
#>  chr1:1549446-1552535, chr1:1051006-1053102, chr1:1240091-1245762,
#> chr1:1333514-1336003, chr1:1309645-1311492, chr1:928630-937949,
#> chr1:1166366-1168282, chr1:1446312-1448163, chr1:1562519-1567986,
#> chr1:1259506-1261414 
BinarizeCounts(atac_small)
#> 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