next_junctions: Get genomic coordinates of possible next donor and acceptor...

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

Get genomic coordinates of possible next donor and acceptor sides.

Description

Get genomic coordinates of possible next donor and acceptor sides.

Usage

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.

TRON-Bioinformatics/splice2neo documentation built on July 27, 2024, 3:25 a.m.