Get genomic coordinates of possible next donor and acceptor sides.

Source: R/annotate_mut_effect.R

Get genomic coordinates of possible next donor and acceptor sides.

next_junctions(var_gr, transcripts, transcripts_gr)

Arguments

var_gr

a GenomicRanges object with variants (of length one). It is assumed that it is named with a unique ID. Usually this is <chr>_<pos>_<alt>.

transcripts

a GRangesList with transcripts defined as GRanges of exons created by GenomicFeatures::exonsBy(txdb, by = c("tx"), use.names = TRUE).

transcripts_gr

a GRanges object with transcript ranges created by GenomicFeatures::transcripts(txdb)

Value

A data.frame with possible upstream and downstream exon coordinates for all overlapping transcripts. The data frame contains the following columns: mut_id, var_nr, tx_chr, tx_id, exon_idx, tx_strand, upstream_start, upstream_end, downstream_start, downstream_end, at_start, at_end.