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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,
  ...
)

Arguments

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`.

Value

The sorted `regions` object with additional annotation columns.