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, SGVariants,
SGFeatureCounts or SGVariantCounts object
subject
TxFeatures object
Value
query with updated txName, geneName
column slots
Details
Annotation is performed at the gene and transcript level.
For transcript-level annotation, query features are assigned all
transcript names associated with matching subject features.
For gene-level annotation, query features are assigned all gene
names associated with subject features that belong to the same
gene (connected component of the splice graph) as 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.