get_intronretention_genomic_alt_pos: Get the alternative position of input junction from an intron...

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

Get the alternative position of input junction from an intron retention event in the genomic sequences

Description

Get the alternative position of input junction from an intron retention event in the genomic sequences

Usage

get_intronretention_genomic_alt_pos(
  tx_lst,
  tx_mod,
  jx,
  intron_retention,
  junc_strand
)

Arguments

tx_lst	transcripts a GRangesList with transcripts defined as GRanges of exons.
tx_mod	modified transcripts a GRangesList with transcripts defined as GRanges of exons.
jx	splice junctions as GRanges objects
intron_retention	logical vector indicating if junctions belong to an intron retention event
junc_strand	Strand direction. Can be "+" or "-".

Value

an integer vector with alternative junction positions of intron retention event

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