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Add SQANTI3 Structural Categories to an Annotation

Source: R/annotation-tools.R
add_sqanti_classification.Rd

Long-read transcript catalogs (IsoSeq, FLAIR, Bambu, StringTie) carry no biotype for novel transcripts. SQANTI3 classifies every isoform against a reference (*_classification.txt: isoform, structural_category, associated_gene, associated_transcript, subcategory, ...). add_sqanti_classification() writes those categories into the transcript_type column of an annotation directory (and the associated reference transcript / gene into source_transcript_id, source_gene_id and gene_name when they are missing), so the SQANTI categories behave like transcript types everywhere in the package (plots, enrichment by category, tx_diversity()). The categories are part of tx_type_palette().

Usage

add_sqanti_classification(x, classification, overwrite_types = TRUE)

Arguments

x

An annotation directory path or an IsoformicExperiment (its annotation directory is modified in place and caches refresh automatically).

classification

Path to the SQANTI3 classification file (tab separated, optionally gzipped) or a data frame with at least the isoform and structural_category columns.

overwrite_types

Logical. Replace existing transcript types (default TRUE); with FALSE only missing types are filled.

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 = "sqanti_demo")
#> ℹ Parsing example.gff3 (GFF) into /tmp/RtmpV2WK1u/sqanti_demo.
tx <- read_parquet(file.path(annot, "annot_data_transcripts.parquet"))
classification <- data.frame(
  isoform = tx$transcript_id[1:3],
  structural_category = c("full-splice_match", "novel_in_catalog", "novel_not_in_catalog"),
  associated_gene = "RBPJ",
  associated_transcript = c(tx$transcript_id[1], "novel", "novel")
)
add_sqanti_classification(annot, classification)
#> ✔ Assigned SQANTI categories to 3 of 72 transcripts in
#>   /tmp/RtmpV2WK1u/sqanti_demo.
tx <- read_parquet(file.path(annot, "annot_data_transcripts.parquet"))
head(tx[, c("transcript_id", "transcript_type")], 4)
#> # A tibble: 4 × 2
#>   transcript_id     transcript_type     
#>   <chr>             <chr>               
#> 1 ENST00000282397.9 full-splice_match   
#> 2 ENST00000615611.4 novel_in_catalog    
#> 3 ENST00000617835.4 novel_not_in_catalog
#> 4 ENST00000543394.2 protein_coding