SGSeq (version 1.0.6)

annotateTxVariants: Annotate transcript variants in terms of canonical events

Description

Annotate transcript variants in terms of canonical events.

Usage

annotateTxVariants(variants)

Arguments

variants

TxVariants object

Value

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

Details

The following events are considered: “SE” (skipped exon), “S2E” (two consecutive exons skipped), “RI” (retained intron), “MXE” (mutually exclusive exons), “A5SS” (alternative 5' splice site), “A3SS” (alternative 3' splice site), “AFE” (alternative first exon), “ALE” (alternative last exon), “AS” (alternative start other than “AFE”) and “AE” (alternative end other than “ALE”).

These 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.