Module diffsplice 

Differential exon usage. Port of limma’s diffSplice and topSplice (diffSplice.R, topSplice.R).

diff_splice takes an exon-level MArrayLM fit (one row per exon) plus a gene-id label per exon, and tests whether each exon’s log-fold-change departs from its gene’s average — i.e. whether exon usage changes between conditions. It returns exon-level moderated t-statistics and gene-level F / Simes / Bonferroni summaries. top_splice collates a single coefficient’s results into a ranked table, mirroring topSplice.

The annotation-frame plumbing of R’s diffSplice (carrying through arbitrary genes columns and detecting which are gene-level) is out of scope for this numeric port: gene and exon identity are carried as plain string labels.

Structs

DiffSplice

Result of diff_splice. Exon-level fields have one row per kept exon (exons belonging to genes with at least two exons), in gene-sorted order; gene-level fields have one row per kept gene.

TopSpliceRow

One row of a top_splice table.

Enums

SpliceSort

top_splice row ordering. Mirrors topSplice’s sort.by argument.

SpliceTest

Which statistic top_splice ranks on. Mirrors topSplice’s test argument.

Functions

diff_splice

diffSplice — test for differential exon usage from an exon-level fit.

top_splice

topSplice — collate one coefficient’s diffSplice results into a ranked table. coef is a 0-based column index. treat_lfc > 0 with SpliceTest::T switches to the TREAT variant (as R does).