annotateSGVariants: Annotate splice variants in terms of canonical events

Description Usage Arguments Details Value Author(s)

View source: R/graphs.R


Annotate splice variants in terms of canonical events.





SGVariants object


The following events are considered:


skipped exon


two consecutive exons skipped


retained intron


mutually exclusive exons


alternative 5' splice site


alternative 3' splice site


alternative first exon


alternative last exon


alternative start other than “AFE”


alternative end other than “ALE”

For events “SE” and “S2E”, suffixes “I” and “S” indicate inclusion and skipping, respectively. For event “RI” suffixes “E” and “R” indicate exclusion and retention, respectively. For events “A5SS” and “A3SS”, suffixes “P” and “D” indicate use of the proximal (intron-shortening) and distal (intron-lengthening) splice site, respectively.

All considered events are binary events defined by two alternative variants. A variant is annotated as a canonical event if it coincides with one of the two variants in the canonical event, and there is at least one variant in the same event that coincides with the second variant of the canonical event.


variants with added metadata column “variantType” indicating canonical event(s)


Leonard Goldstein

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.