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

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

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