annotateRegions: annotateRegions

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

annotateRegions

Description

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.

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.