Filter to Genes with Significant Orthologous Splice Junctions

Subsets a SummarizedExperiment to retain only orthologous splice junctions from genes (orthogroups) that contain at least one significant orthologous splice junction.

Usage

filterSignificantGenes(se)

Arguments

se

SummarizedExperiment. Orthologous splice junction data with a significant column in mcols (from runDS).

Value

A SummarizedExperiment containing only orthologous splice junctions from genes with at least one significant result. Genes without any significant orthologous splice junctions are removed entirely.

Details

This function is useful for downstream analyses that focus on genes showing differential splicing. It uses seqnames(se) as the gene/orthogroup identifier.

The filtering logic:

1. Identify genes containing at least one significant orthologous splice junction

2. Keep all orthologous splice junctions (significant or not) from those genes

3. Remove all orthologous splice junctions from genes with no significant results

See also

runDS to identify significant orthologous splice junctions, annotateOSJ to annotate filtered results.

Examples

if (FALSE) { # \dontrun{
# After differential splicing analysis
se <- runDS(data, se, methodName = "phyloDEOU")

# Keep only genes with significant orthologous splice junctions
se_sig <- filterSignificantGenes(se)

# Check reduction
length(se)      # All orthologous splice junctions
length(se_sig)  # Orthologous splice junctions from significant genes only
} # }