constructAlternativeEvents: Construct alternative transcription events form a list of...
In kauralasoo/reviseAnnotations: What the package does (short line)

Description Usage Arguments Value Author(s)

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.

1 2	constructAlternativeEvents(granges_list, gene_id, max_internal_diff = 10, max_start_end_diff = 25)

`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.

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

Kaur Alasoo

kauralasoo/reviseAnnotations documentation built on May 20, 2019, 7:41 a.m.