Structural and Coding Features of Transcripts — transcript

Computes, for every assayed transcript, features that go beyond the biotype label, from the exon and CDS coordinates of the annotation:

Ends: tss_pos, tes_pos (genomic positions of the transcription start and end), tss_group and tes_group (integer labels of alternative promoters / 3' ends within the gene; starts or ends closer than end_window bp share a group).
ORF: has_cds, cds_complete (FALSE when the annotation flags an incomplete CDS with cds_start_NF/cds_end_NF), orf_length (nt), utr5_length, utr3_length.
NMD rule: stop_to_last_junction, the distance in transcript coordinates from the stop codon to the last exon-exon junction, and nmd_predicted (TRUE when that distance exceeds nmd_rule nt, the classical 50-55 nt rule).
Comparison with the canonical isoform: canonical_transcript_id (the MANE Select / Ensembl canonical transcript of the gene, else the transcript with the longest CDS, else the longest transcript), orf_fraction_of_canonical and cds_differs_from_canonical.
Splicing events relative to the canonical isoform (see splicing_events()): n_skipped_exons, n_novel_exons, n_retained_introns, n_alt_5ss, n_alt_3ss, alt_first_exon, alt_last_exon.

splicing_events() returns the event counts alone; both are cached per object. The data-frame methods accept the exon table of an annotation (see exon_table()) joined with the transcript columns.

Usage

transcript_features(
  self,
  gene_name = NULL,
  nmd_rule = 50,
  end_window = 50,
  ...
)

splicing_events(self, gene_name = NULL, ...)

Arguments

self: An IsoformicExperiment or an annotation directory path.
gene_name: Optional genes (names or IDs) to restrict the result to.
nmd_rule: Distance in nucleotides from the stop codon to the last junction above which NMD is predicted (default 50).
end_window: Distance in bp within which transcription starts (or ends) are grouped as the same promoter (or 3' end); default 50.
...: Passed on to methods.

Value

A tibble with one row per transcript.

Examples

iso <- example_isoformic()
feats <- transcript_features(iso, gene_name = "RBPJ")
feats[, c("transcript_name", "orf_length", "nmd_predicted", "tss_group", "n_skipped_exons")]
#> # A tibble: 10 × 5
#>    transcript_name orf_length nmd_predicted tss_group n_skipped_exons
#>    <chr>                <int> <lgl>             <int>           <int>
#>  1 RBPJ-222               283 FALSE                 1               2
#>  2 RBPJ-201              1503 FALSE                 2               0
#>  3 RBPJ-206              1503 FALSE                 3               0
#>  4 RBPJ-225                NA FALSE                 4               0
#>  5 RBPJ-204              1464 FALSE                 5               0
#>  6 RBPJ-205              1461 FALSE                 5               0
#>  7 RBPJ-214              1398 FALSE                 6               0
#>  8 RBPJ-208              1149 FALSE                 7               1
#>  9 RBPJ-202              1461 FALSE                 7               0
#> 10 RBPJ-210                NA FALSE                 8               0
splicing_events(iso, gene_name = "EGFR")
#> # A tibble: 7 × 12
#>   transcript_id     transcript_name gene_id     gene_name canonical_transcript…¹
#>   <chr>             <chr>           <chr>       <chr>     <chr>                 
#> 1 ENST00000275493.7 EGFR-201        ENSG000001… EGFR      ENST00000275493.7     
#> 2 ENST00000455089.5 EGFR-207        ENSG000001… EGFR      ENST00000275493.7     
#> 3 ENST00000344576.6 EGFR-203        ENSG000001… EGFR      ENST00000275493.7     
#> 4 ENST00000420316.6 EGFR-204        ENSG000001… EGFR      ENST00000275493.7     
#> 5 ENST00000459688.1 EGFR-208        ENSG000001… EGFR      ENST00000275493.7     
#> 6 ENST00000638463.1 EGFR-211        ENSG000001… EGFR      ENST00000275493.7     
#> 7 ENST00000485503.1 EGFR-210        ENSG000001… EGFR      ENST00000275493.7     
#> # ℹ abbreviated name: ¹canonical_transcript_id
#> # ℹ 7 more variables: n_skipped_exons <int>, n_novel_exons <int>,
#> #   n_retained_introns <int>, n_alt_5ss <int>, n_alt_3ss <int>,
#> #   alt_first_exon <lgl>, alt_last_exon <lgl>