Set motif data — SetMotifData • Signac

Set motif matrix for given assay

Usage

SetMotifData(object, ...)

# S3 method for class 'Motif'
SetMotifData(object, slot, new.data, ...)

# S3 method for class 'ChromatinAssay5'
SetMotifData(object, slot, new.data, ...)

# S3 method for class 'Seurat'
SetMotifData(object, assay = NULL, ...)

Arguments

object: A Seurat object
...: Arguments passed to other methods
slot: Name of slot to use
new.data: motif matrix to add. Should be matrix or sparse matrix class
assay: Name of assay whose data should be set

Value

Returns a SeuratObject::Seurat() object

Examples

motif.obj <- SeuratObject::GetAssayData(
  object = atac_small[["peaks"]], slot = "motifs"
)
SetMotifData(object = motif.obj, slot = "data", new.data = matrix(1:2))
#> A Motif object containing 1 motifs in 2 regions
new.data <- matrix(sample(c(0, 1),
  size = nrow(atac_small[["peaks"]]) * 10,
  replace = TRUE
), nrow = nrow(atac_small[["peaks"]]))
rownames(new.data) <- rownames(atac_small[["peaks"]])
SetMotifData(
  object = atac_small[["peaks"]], slot = "data", new.data = new.data
)
#> Warning: Overwriting motif information
#> GRangesAssay data with 100 features for 100 cells
#> Variable features: 0 
#> Annotation present: TRUE 
#> Fragment files: 0 
#> Motifs present: TRUE 
#> Links present: 0 
#> Region aggregation matrices: 0
motif.matrix <- GetMotifData(object = atac_small)
SetMotifData(
  object = atac_small,
  assay = "peaks",
  slot = "data",
  new.data = motif.matrix
)
#> Warning: Overwriting motif information
#> An object of class Seurat 
#> 150 features across 100 samples within 2 assays 
#> Active assay: peaks (100 features, 0 variable features)
#>  2 layers present: counts, data
#>  1 other assay present: RNA
#>  2 dimensional reductions calculated: lsi, umap