Get the longest transcript per gene — .get_longest_utr • SeedMatchR

.get_longest_utr will extract the longest transcript per gene in a GenomicRanges::GRangesList using an ensembldb::EnsDb object. The GenomicFeatures::transcriptLengths() function is used to calculate the 3' UTR lengths for each transcript in the ensembldb::EnsDb object.

Usage

.get_longest_utr(utr.grlist, txdb, filter = NULL)

Arguments

utr.grlist: A GenomicRanges::GRangesList of UTR exons grouped by tx_id
txdb: An ensembldb::EnsDb object
filter: Optional AnnotationFilter::AnnotationFilterList object

Value

A GenomicRanges::GRangesList filtered containing the longest 3' UTR per gene in the ensembldb::EnsDb object that pass filters in the optional AnnotationFilter::AnnotationFilterList

Examples

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

features = GenomicFeatures::threeUTRsByTranscript(annodb$txdb)

longest.tx = SeedMatchR:::.get_longest_tx(features, annodb$txdb)
}