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, ...)A Seurat object
Arguments passed to other methods
Name of assay to use. Can be a list of assays, and binarization will be applied to each.
Display messages
Returns a Seurat object
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']])
#> ChromatinAssay data with 323 features for 100 cells
#> Variable features: 323
#> Genome: hg19
#> Annotation present: TRUE
#> Motifs present: TRUE
#> Fragment files: 0
BinarizeCounts(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