parse_star_sj: Imports "*SJ.out.tab" from STAR and transforms the raw output...

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

Imports "*SJ.out.tab" from STAR and transforms the raw output into standardized junction output format.

Description

Imports "*SJ.out.tab" from STAR and transforms the raw output into standardized junction output format.

Usage

parse_star_sj(path, keep_unstranded = FALSE)

Arguments

path	The path to STAR SJ.out.tab
keep_unstranded	Logical, to keep junctions without strand annotation. If FALSE (default) junctions without strand annotation "*" are filtered out, otherwise they are considered as two separate junctions with "+" and "-" strand.

Value

A tibble in standardized junction format

Examples

path <-  system.file("extdata", "test_star_SJ.out.tab", package = "splice2neo")
parse_star_sj(path)

TRON-Bioinformatics/splice2neo documentation built on Nov. 9, 2024, 5:28 p.m.