annotate: Annotation with respect to transcript features

In SGSeq: Splice event prediction and quantification from RNA-seq data

Description

Features in query are assigned transcript names and gene names of structurally compatible features in subject (see below). If a feature in query does not match any features in subject, its geneName inherits from connected annotated features.

Usage

annotate(query, subject)

Arguments

query	SGFeatures, SGVariants, SGFeatureCounts or SGVariantCounts object
subject	TxFeatures object

Details

Feature matching is performed as follows: Query splice junctions are matched with identical subject splice junctions. Query splice sites are matched with splice sites implied by subject splice junctions. Query exon bins are matched with overlapping subject exons. Spliced boundaries of query exon bins must match spliced subject exon boundaries. Query exon bins cannot extend across spliced subject exon boundaries.

Value

query with updated txName, geneName column slots

Author(s)

Leonard Goldstein

Examples

sgf_annotated <- annotate(sgf_pred, txf_ann)
sgv_annotated <- annotate(sgv_pred, txf_ann)

SGSeq documentation built on Nov. 8, 2020, 8:31 p.m.