Compares the Pfam domains of every isoform with those of the canonical
isoform of its gene, using the APPRIS SPADE domain coordinates (frozen
dataset appris_domains, frozen_data). For isoforms present in APPRIS
the domain sets are compared directly. For other isoforms (novel
transcripts) the genomic span of each canonical domain is projected onto
the isoform: a domain is retained when the isoform covers the same
exonic bases over the domain span and its ORF (see transcript_orfs(),
or the annotated CDS) extends over it without a frameshift, partial
when only part of the span is covered, and lost otherwise.
An altered_productive isoform that keeps all domains of the canonical
protein is a milder event than one that loses a domain; the
domain_retention_fraction column grades this and is included in
transcript_productivity() output when the dataset is available.
Arguments
Value
A tibble with one row per transcript: n_domains_canonical,
n_retained, n_partial, n_lost, domains_lost (Pfam names) and
domain_retention_fraction (NA when the canonical isoform has no
domain).
Examples
if (FALSE) { # \dontrun{
iso <- example_isoformic()
domain_retention(iso, gene_name = "RBPJ")
} # }