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, ... )
A Seurat or ChromatinAssay object
Arguments passed to other methods
BSgenome object or any other object supported by
showMethods("getSeq") to get the list of all
supported object types.
Name of a motif stored in the assay to footprint. If not supplied, must supply a set of regions.
Key to store positional enrichment information under.
A set of genomic ranges containing the motif instances. These should all be the same width.
Name of assay to use
Number of bases to extend upstream
Number of bases to extend downstream
Find the expected number of insertions at each position given the local DNA sequence context and the insertion bias of Tn5
Restrict motifs to those that fall in peaks