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Attach External Productivity Evidence to an Annotation

Source: R/productivity-evidence.R
productivity_evidence.Rd

These functions add evidence columns to the transcript table of the annotation directory of x from the frozen datasets (frozen_data), so that transcript_productivity() can use observed translation and decay instead of rules alone. Identifiers are matched without version.

  • add_appris() adds appris_annotation (PRINCIPAL:1 ... ALTERNATIVE:2, MINOR), appris_principal, appris_score and the method scores (firestar_residues, matador_structure, corsair_conservation, spade_domain_score, thump_tm_helices, trifid_score). Principal isoforms are productive evidence.

  • add_riboseq_orfs() adds riboseq_n_orfs (Ribo-seq ORFs compatible with the transcript's exon structure), riboseq_orf_types, riboseq_main_orf (TRUE when a translated ORF coincides with the transcript's own ORF, from transcript_orfs() when sequences are available or else from the annotated CDS) and riboseq_uorf. A translated main ORF is productive evidence. Phase 1 ORFs list their compatible transcripts; all ORFs are also matched by exon-block compatibility (every block inside an exon, consecutive blocks in consecutive exons, internal block boundaries on exon boundaries).

  • add_nmd_exons() adds nmd_validated_exon, TRUE when the transcript contains an exon with the exact coordinates of an NMD-inducing cassette exon validated by NMD inhibition (Karousis et al. 2021), or is one of the listed NMD isoforms. This is unproductive evidence.

Each function returns the annotation directory path invisibly and invalidates the object caches of x (the next call to a method rereads the annotation).

Usage

add_appris(x, table = NULL)

add_riboseq_orfs(x, table = NULL)

add_nmd_exons(x, table = NULL)

Arguments

x

An annotation directory path or an IsoformicExperiment.

table

A data frame with the dataset, or a path to its Parquet file; NULL (default) fetches the frozen dataset with fetch_frozen_data().

Value

The annotation directory path, invisibly.

Examples

if (FALSE) { # \dontrun{
iso <- example_isoformic()
add_appris(iso)
add_riboseq_orfs(iso)
add_nmd_exons(iso)
prod <- transcript_productivity(iso, gene_name = "RBPJ")
prod[, c("transcript_name", "productivity", "reason", "source")]
} # }