Count fragments surrounding motif sites

Count the number of sequenced DNA fragments in a region surrounding each instance of a given DNA sequence motif.

MotifCounts(
  object,
  motifs,
  flanking.region = 1000,
  assay = NULL,
  verbose = TRUE,
  ...
)

Arguments

object: A Seurat object
motifs: A list of DNA sequence motif names. One matrix will be generated for each motif
flanking.region: Amount of sequence to include surrounding the motif itself
assay: Name of assay to use. Must be a ChromatinAssay
verbose: Display messages
...: Additional arguments passed to FeatureMatrix

Returns a list of sparse matrices