annotate: Annotation with respect to transcript features
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
Value
query with updated txName, geneName
column slots
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.