Convert transcript features to splice graph features
Convert transcript features (predicted from RNA-seq data or extracted from transcript annotation) to splice graph features.
Logical indicating whether transcript features should be coerced to splice graph features without disjoining exons and omitting splice donor and acceptor sites
Splice junctions are unaltered. Exons are disjoined into non-overlapping exon bins. Adjacent exon bins without a splice site at the shared boundary are merged.
Entries for splice donor and acceptor sites (positions immediately upstream and downstream of introns, respectively) are added.
In the returned
SGFeatures object, column
values “J” (splice junction), “E” (exon bin),
“D” (splice donor) or “A” (splice acceptor).
splice3p indicate mandatory
splices at the 5' and 3' end of exon bins, respectively
(determining whether reads overlapping exon boundaries must be
spliced at the boundary to be considered compatible).
TRUE if the first (last)
position of the exon coincides with a splice acceptor (donor)
and it is not adjacent to a neighboring exon bin.
Each feature is assigned a unique feature and gene identifier,
stored in columns
respectively. The latter indicates features that belong to the
same gene, represented by a connected component in the splice graph.
sgf <- convertToSGFeatures(txf_ann)