Footprint | R Documentation |
Compute the normalized observed/expected Tn5 insertion frequency for each position surrounding a set of motif instances.
Footprint(object, ...) ## S3 method for class '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 class '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. These should all be the same width. |
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
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