add_tx: Annotate splice junctions with all possible transcript IDs in...

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

Annotate splice junctions with all possible transcript IDs in the given genomic region.

Description

Annotate splice junctions with all possible transcript IDs in the given genomic region.

Usage

add_tx(df, transcripts)

Arguments

df	A data.frame with splice junctions in rows and at least the columns: junc_id junction id consisting of genomic coordinates
transcripts	GRangesList of transcripts

Value

A data.frame as the input but with potentially multiple rows and with the additional column(s):

• tx_id the ID of the affected transcript

• tx_lst a list of GRanges with the transcript

Examples

junc_df <- tibble::tibble(
  junc_id = c("chr2:152389996-152392205:-", "chr2:152389996-152390729:-",
              "chr2:152389955-152389956:-")
)

add_tx(junc_df, toy_transcripts)

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