getASCons.RdQuantify sequence conservation scores of alternatively-spliced exons.
# S4 method for factR
getAScons(object, db = "phastCons", type = "exon", padding = 50)factR object
Database to extract sequence conservation. Can be "phastCons" (Default) or "phylop"
Feature to quantify conservation. Can be one of the following:
"exon" : Sequence conservation of the entire exon
"flanks" : Conservation of sequences flanking exons
"upstream" : Conservation of sequences upstream of exons
"downstream" : Conservation of sequences downstream of exons
Additional width to pad the sequence by. For cons_type "exons" and "flanks", padding will be added on both sides.
factRObject with additional columns in AS metadata.
The name of column(s) created will be "Cons.<type>.pad<padding>"
By default, this function quantifies the sequence conservation of the entire exon together with 50 base-pair flanking sequence using the phastCons database. Alternatively, this function can also quantify the mean conservation scores of sequences flanking exons, or sequences upstream/downstream of alternative exons.
The `padding` argument has different meaning depending on the `type` input. If `type` is "exon", then `padding` refers to the amount of intronic sequences on both sides of the exon to include in the quantification. If `type` is "flanks", "upstream" or "downstream", then `padding` refers to the amount of intronic sequnce to