Compute Signac insertion bias and footprints with an explicit sequence reference. No reference is downloaded. Existing cached footprints are never overwritten.
Usage
RunATACFootprint(
object,
genome,
genome.id,
bias.region,
motifs,
assay = NULL,
upstream = 250L,
downstream = 250L,
in.peaks = FALSE,
verbose = TRUE
)Arguments
- object
A Seurat object containing a ChromatinAssay.
- genome
A loaded BSgenome or indexed Rsamtools FaFile.
- genome.id
Verified reference label matching the assay.
- bias.region
One explicit chromosome interval string, for example `chr1-4-1000000`. It must fit the reference. Bias estimation requires adequate coverage of all hexamers and can fail on small datasets.
- motifs
Unique motif IDs present in the selected assay's positions.
- assay
Source assay; defaults to the active assay.
- upstream, downstream
Nonnegative flanking widths (at least 50 each).
- in.peaks
Restrict motif instances to peaks.
- verbose
Print progress.
Value
A Seurat object with positionEnrichment and a `scop_footprints` receipt in assay Misc. Input counts, cells and default assay are preserved. At least two assay cells are required. A receipt is a snapshot; recalculate after changing cells, peaks, fragments or reference.
Details
Requires indexed local fragment files with complete cell/barcode mappings. Bias is recalculated using the explicit region, never silently reused from another reference. Estimation errors are preserved. Footprints summarize Tn5 insertion patterns, not proven TF binding or causality. Factors sharing a motif cannot be distinguished by this analysis.