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Annotates a GRanges object with nearby features in another GRanges object

annotate_nearby_features.Rd

Distance is measured as distance from end and start depending whether the target locus is downstream or upstream.

Usage

annotate_nearby_features(
  gr,
  feat_gr,
  name_field,
  distance_cutoff = 2500,
  ignore.strand = TRUE
)

Arguments

gr

GRanges object to be annotated

feat_gr

GRanges features to be annotated.

name_field

Name of the column that contains the annotation name in feat_gr

distance_cutoff

Maximum distance around the promoter of the feature

ignore.strand

Ignore strand when annotating. Default FALSE

Value

A GRanges object with a nearby_features field in it containing names of overlapping features in that distance range (separated by commas)

Examples


features_gr <- GenomicRanges::GRanges(
  seqnames = c("chr1", "chr1"),
  IRanges::IRanges(c(10,22), c(20,30)),
  strand = c("-", "-"),
  name = c("Feat_A", "Feat_B")
)

gr <- GenomicRanges::GRanges(
  seqnames = c("chr1"),
  IRanges::IRanges(15, 25),
  strand = "+"
)

annotate_nearby_features(gr, features_gr, "name", ignore.strand = TRUE)
#> GRanges object with 1 range and 1 metadata column:
#>       seqnames    ranges strand |    annotation
#>          <Rle> <IRanges>  <Rle> |   <character>
#>   [1]     chr1     15-25      + | Feat_A,Feat_B
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths