Find transcripts covering given splice junction breakpoints

This function identifies transcripts that cover specified junction breakpoints.

Usage

bp_junction_transcript_overlap(bp_junctions = NULL, ref_data = NULL)

Arguments

bp_junctions

A data frame with columns:

• BP_CHROM: Chromosome of the breakpoint junction

• BP_POSITION: Chromosome position of the breakpoint junction

ref_data

PCGR reference data bundle (list)

Value

A data frame with columns:

• CHROM: Chromosome of the breakpoint junction

• BP_POSITION: Position of the breakpoint junction

• ENSEMBL_TRANSCRIPT_ID: Ensembl transcript ID covering the splice junction

• ENSEMBL_GENE_ID: Ensembl gene ID

• GENE_BIOTYPE: Biotype of the transcript

• TRANSCRIPT_START: Start position of the transcript

• TRANSCRIPT_END: End position of the transcript