constructAlternativeEventsWrapper: Apply constructAlternativeEvents() to an gene_id and metadata...

In kauralasoo/txrevise: Extend and revise transcript annotatons.

Apply constructAlternativeEvents() to an gene_id and metadata objects. Extend truncated transcripts first.

Description

Apply constructAlternativeEvents() to an gene_id and metadata objects. Extend truncated transcripts first.

Usage

constructAlternativeEventsWrapper(gene_id, gene_metadata, exons, cdss,
  max_internal_diff = 10, max_start_end_diff = 25, fill_internal)

Arguments

gene_id	Focal gene id.
gene_metadata	Tibble containing gene metadata from the prepareAnnotations script.
exons	List of annotated exons
cdss	List of annotated CDSs
max_internal_diff	maximal internal difference between two evets for them to be considered the same.
max_start_end_diff	maximal difference at the start and end of two events for them to be considered
fill_internal	Fill internal exons for alternative promoter and 3'end events. the same.

Value

Three-level list. First level correspond the each set of overlapping transcripts, second level contains lists of downstream, upstream and contained alternative transcription events.

kauralasoo/txrevise documentation built on March 31, 2022, 12:03 p.m.