Attach Extra Columns to the Annotation Tables

Joins columns of an external per-transcript or per-gene table into the annotation directory (persisted in the Parquet tables, so every object using the annotation sees them and caches refresh automatically). This is the hook for evidence that the package does not compute itself: FANTOM CAGE clusters, GTEx dominant isoforms per tissue, Ribo-seq translation calls, NMD-inhibition responses, protein domain retention, long-read full-length counts. A column named productivity_evidence with values "productive" / "unproductive" overrides the call of transcript_productivity().

Usage

add_annotation_columns(
  x,
  table,
  level = c("transcript", "gene"),
  by = NULL,
  prefix = NULL
)

Arguments

x

An annotation directory path or an IsoformicExperiment.

table

A data frame, or a path to a tabular file readable by read_tabular().

level

"transcript" (default) or "gene".

by

Name of the key column in table; defaults to transcript_id/gene_id, or the first column.

prefix

Optional prefix added to the new column names.

Value

The annotation directory path, invisibly.

Examples

gff <- system.file("extdata", "example.gff3", package = "isoformic")
annot <- prepare_isoformic_annotation(gff, output_path = tempdir(), annot_name = "evidence_demo")
#> ℹ Parsing example.gff3 (GFF) into /tmp/RtmpV2WK1u/evidence_demo.
tx <- read_parquet(file.path(annot, "annot_data_transcripts.parquet"))
evidence <- data.frame(
  transcript_id = tx$transcript_id[1:2],
  riboseq_translated = c(TRUE, FALSE),
  productivity_evidence = c("productive", "unproductive")
)
add_annotation_columns(annot, evidence)
#> ✔ Added 2 columns (riboseq_translated and productivity_evidence) for 2 of 72
#>   transcripts in /tmp/RtmpV2WK1u/evidence_demo.
tx <- read_parquet(file.path(annot, "annot_data_transcripts.parquet"))
head(tx[, c("transcript_id", "riboseq_translated")], 3)
#> # A tibble: 3 × 2
#>   transcript_id     riboseq_translated
#>   <chr>             <lgl>             
#> 1 ENST00000282397.9 TRUE              
#> 2 ENST00000615611.4 FALSE             
#> 3 ENST00000617835.4 NA