deprecated: Deprecated function: Annotate junctions using reference...

In dzhang32/dasper: Detecting abberant splicing events from RNA-sequencing data

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.

dzhang32/dasper documentation built on Dec. 14, 2024, 8:33 p.m.