annotate_junc_ref {dasper} | R Documentation

## Deprecated function: Annotate junctions using reference annotation

### Description

`annotate_junc_ref` is deprecated, please use `junction_annot` instead. annotates junctions by whether their start and end position precisely overlaps with a known exon boundary. Using this information along with the strand, junctions are categorised into "annotated", "novel_acceptor", "novel_donor", "novel_combo", "novel_exon_skip", "ambig_gene" and "none".

### Usage

    annotate_junc_ref(junc_metadata, gtf)

    .get_ref_exons_annot(
      junc_metadata,
      ref_exons,
      ref_cols = c("strand", "gene_name", "gene_id", "transcript_id", "exon_id")
    )

    .tidy_junc_annot(
      junc_metadata,
      cols_to_merge = c("strand", "gene_name", "gene_id")
    )

    .classify_junc(junc_metadata, ref_junc)

    .get_gr_for_start_end(gr)

    .merge_lists(x, y)

### Arguments

`junc_metadata` | junction metadata in a GRanges-class format, the essential component being the junction co-ordinates.
`gtf` | either path to gtf or object of class `ensemblGenome` loaded using `refGenome`.

### Value

junction metadata as a GRanges-class object with additional columns that detail overlapping genes/transcripts/exons and junction categories.

[Package dasper version 1.4.0 Index]