annotate_exon_idx: Annotate splice junctions- transcripts combination and...

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

Annotate splice junctions- transcripts combination and transcripts with exon details

Description

Annotate splice junctions- transcripts combination and transcripts with exon details

Usage

annotate_exon_idx(df)

Arguments

df	A data.frame with junctions- transcripts combination in rows. junc_id junction id consisting of genomic coordinates tx_id transcript id tx_lst a list of GRanges with the transcript and additional columns.

Value

A data.frame as the input but with more annotations in the following columns:

• pos_left_on_exon_end exon index if junction start matches with exon end coordinate

• pos_right_on_exon_start exon index if junction end matches with exon start coordinate

• pos_left_on_exon_idx exon index in transcript if junction start overlaps exon

• pos_right_on_exon_idx exon index in transcript if junction end overlaps exon

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