constructAlternativeEvents: Construct alternative transcription events form a list of...

In kauralasoo/txrevise: Extend and revise transcript annotatons.

Construct alternative transcription events form a list of transcripts.

Description

Also works if not all transcripts of a gene overlap with each other. In this case the transcripts are first split into overlapping sets (cliques in the transcript overlap graph) and events are calculated within each set independently.

Usage

constructAlternativeEvents(granges_list, gene_id, max_internal_diff = 10,
  max_start_end_diff = 25)

Arguments

granges_list	List of GRanges objects containing the exon coordinates of each transcript (One object per transcript).
gene_id	ID of the the gene to which the transcripts belong to.
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 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.

Author(s)

Kaur Alasoo

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