liftover_junc_id: LiftOver junction IDs using the liftOver tool

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

LiftOver junction IDs using the liftOver tool

Description

This can be used to liftOver junctions to personalized genome coordinates.

Usage

liftover_junc_id(junc_df, chain_file)

Arguments

junc_df	a data.frame with at least one column junc_id containing junction IDs
chain_file	path to a chain file for the UCSC liftOver tool. See also liftOver

Value

a data.frame like the input junc_df with the following additional columns:

• liftover_successful a logical vector indicating if the liftOver was successful and lifted junction positions build valid genomic intervals and not single positions.

• liftover_unique a logical vector indicating if the liftOver was unique (1-to-1 correspondence).

• junc_id_lifted_collapsed a character vector with the lifted junction IDs. Multiple IDs are separated by |. NA represent junc_ids that could not be lifted.

• junc_id_lifted a character vector with a unique lifted junction IDs. Potentially multiple lifted IDs are combined by the minimal start and maximal end coordinate. NA represent junc_ids that could not be lifted.

Examples

chain_file = system.file(package="liftOver", "extdata", "hg38ToHg19.over.chain")
junc_df <- toy_junc_df
liftover_junc_id(junc_df, chain_file)

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