Compute the normalized observed/expected Tn5 insertion frequency for each position surrounding a set of motif instances.
Footprint(object, ...) # S3 method for ChromatinAssay Footprint( object, genome, motif.name = NULL, key = motif.name, regions = NULL, assay = NULL, upstream = 250, downstream = 250, compute.expected = TRUE, in.peaks = FALSE, verbose = TRUE, ... ) # S3 method for Seurat Footprint( object, genome, regions = NULL, motif.name = NULL, assay = NULL, upstream = 250, downstream = 250, in.peaks = FALSE, verbose = TRUE, ... )
| object | A Seurat or ChromatinAssay object |
|---|---|
| ... | Arguments passed to other methods |
| genome | A |
| motif.name | Name of a motif stored in the assay to footprint. If not supplied, must supply a set of regions. |
| key | Key to store positional enrichment information under. |
| regions | A set of genomic ranges containing the motif instances |
| assay | Name of assay to use |
| upstream | Number of bases to extend upstream |
| downstream | Number of bases to extend downstream |
| compute.expected | Find the expected number of insertions at each position given the local DNA sequence context and the insertion bias of Tn5 |
| in.peaks | Restrict motifs to those that fall in peaks |
| verbose | Display messages |
Returns a Seurat object