SGSeq (version 1.6.2)

annotateSGVariants: Annotate splice variants in terms of canonical events

Description

Annotate splice variants in terms of canonical events.

Usage

annotateSGVariants(variants)

Arguments

variants

SGVariants object

Value

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

Details

The following events are considered:

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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.