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Srivastava Lab

Build a junction-ID event table from SUPPA2 events

Source: R/events.R
BuildJunctionEvents.Rd

SUPPA2 .ioe files describe each splicing event with transcript IDs, but junction mode needs the inclusion/exclusion features to be junction IDs that match a STARsolo SJ matrix. The genomic coordinates of every defining junction are, however, fully encoded in the SUPPA2 event_id (e.g. SE:chr1:804222-804776:804966-807217:+). This function parses that grammar per event type and emits the chr-start-end-strand junction IDs Matisse expects, returning the data.frame that CreateMatisseObject accepts via events. This is a deterministic coordinate adapter, not a heuristic event caller.

Usage

BuildJunctionEvents(
  ioe_files,
  event_types = c("SE", "A3", "A5", "MX", "AF", "AL"),
  junction_universe = NULL,
  intron_offset = "auto",
  verbose = TRUE
)

Arguments

ioe_files

Character vector of SUPPA2 .ioe file path(s).

event_types

Character vector of event types to keep. Default: c("SE", "A3", "A5", "MX", "AF", "AL").

junction_universe

Optional character vector of observed junction IDs (e.g. colnames(ReadSTARsoloSJ(...))). Used to auto-calibrate intron_offset and to report match rate. Default: NULL.

intron_offset

Either "auto" (calibrate against junction_universe; falls back to c(1L, 1L) if absent) or an integer vector c(left, right) added to the donor / subtracted from the acceptor exon-boundary coordinate. Default: "auto".

verbose

Logical. Print progress. Default: TRUE.

Value

A data.frame with columns event_id, gene_id, chr, strand, event_type, inclusion_features, exclusion_features (the last two semicolon-separated junction IDs).

Details

Coordinate convention. SUPPA2 reports exon-boundary positions (last base of the donor exon, first base of the acceptor exon). STARsolo SJ reports the first/last intronic base. The two differ by a fixed offset (intron = [donor + 1, acceptor - 1]). When junction_universe is supplied and intron_offset = "auto", the offset is calibrated by maximising overlap with the observed STARsolo junctions; otherwise the standard c(1L, 1L) is used.

Supported event types. SE, A3, A5, MX, AF, AL. RI (retained intron) is not junction-quantifiable - intron retention has no supporting split junction - and is dropped with a warning if requested.

See also

ReadSTARsoloSJ, CreateMatisseObject.

Examples

if (FALSE) { # \dontrun{
jxn    <- ReadSTARsoloSJ("Solo.out/SJ/raw", cells = colnames(seu))
events <- BuildJunctionEvents(
  list.files("events", "\\.ioe$", full.names = TRUE),
  junction_universe = colnames(jxn)
)
obj <- CreateMatisseObject(seu, junction_counts = jxn, events = events)
} # }