annotateRegions — annotateRegions • epiwraps

Annotates a GRanges on the basis of an annotation object (e.g. EnsDb).

Usage

annotateRegions(
  regions,
  anno,
  proximal = c(2500, 1000),
  filter = AnnotationFilterList(),
  extra = list(),
  ignore.strand = TRUE,
  ...
)

regions: A GRanges object
anno: An annotation object, such as an EnsDb) object, a TxDb object, or a GRanges object of a GENCODE-like gtf or the path to such a file.
proximal: The threshold(s) for TSS proximal regions. Multiple values will result in multiple class factor levels.
filter: An AnnotationFilter to filter transcripts. Only used if `anno` is an EnsDb).
extra: An optional named list of GRanges for additional overlaps. Each list element will create an additional binary metadata column.
ignore.strand: Whether to ignore the strand for the overlap with elements of `extra` (default TRUE).
...: Passed to overlapsAny for the overlaps with `extra`.

The sorted `regions` object with additional annotation columns.