Construct a Motif object containing DNA sequence motif information and add it to an existing Seurat object or ChromatinAssay. If running on a Seurat object, AddMotifs will also run RegionStats to compute the GC content of each peak and store the results in the feature metadata.

AddMotifs(object, ...)

# S3 method for default
AddMotifs(object, genome, pfm, verbose = TRUE, ...)

# S3 method for ChromatinAssay
AddMotifs(object, genome, pfm, verbose = TRUE, ...)

# S3 method for Seurat
AddMotifs(object, genome, pfm, assay = NULL, verbose = TRUE, ...)

Arguments

object

A Seurat object or ChromatinAssay object

...

Additional arguments passed to other methods

genome

A BSgenome, DNAStringSet, FaFile, or string stating the genome build recognized by getBSgenome.

pfm

A PFMatrixList or PWMatrixList object containing position weight/frequency matrices to use

verbose

Display messages

assay

Name of assay to use. If NULL, use the default assay

Value

When running on a ChromatinAssay or Seurat object, returns a modified version of the input object. When running on a matrix, returns a Motif object.