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

Description Usage Arguments Value Author(s)

View source: R/constructAlternativeEvents.R

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

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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/reviseAnnotations documentation built on Oct. 22, 2017, 3:13 p.m.