annotate: Annotation with respect to transcript features
Description
Features in query are annotated with respect to transcript
features in subject.
Usage
annotate(query, subject)
Arguments
query
SGFeatures, TxVariants,
SGFeatureCounts or TxVariantCounts object
subject
TxFeatures object
Value
query with updated txName, geneName
column slots
Details
Annotation happens at two levels: For feature-centric annotation,
query features are assigned all transcript names associated with any
matching subject features. For gene-centric annotation, query features
are assigned all gene names associated with subject features that are
part of the same gene (connected component in the splice graph)
as any matching query features.
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.