Extract GenomicRanges::GRangesList of 3' UTRs — get_3UTR

get_3UTR_granges leverages the GenomicFeatures::threeUTRsByTranscript() function to extract 3' UTR regions from a given ensembldb::EnsDb object.

Usage

get_3UTR_granges(
  txdb,
  filter = NULL,
  longest.utr = FALSE,
  reduce.features = FALSE
)

Arguments

txdb: An ensembldb::EnsDb object
filter: An AnnotationFilter::AnnotationFilterList for selecting transcripts
longest.utr: Reduce annotations to the longest UTR per gene
reduce.features: Reduce 3' UTRs to non-overlapping intervals across all transcripts per gene.

Value

A GenomicRanges::GRangesList object representing the genomic features of interest. Results are returned grouped by transcript, unless longest.utr is TRUE, then results are grouped by gene.

Examples

if (FALSE) { # interactive()
annodb <- SeedMatchR::load_species_anno_db("hg38")

features <- SeedMatchR::get_3UTR_granges(annodb$txdb)
}