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Display the Context of an Orthologous Splice Junction

showOSJ.Rd

Prints a formatted summary of a single orthologous splice junction from an object returned by annotateOSJ. The report gathers the projected reference-species coordinates (seqnames, strand, donor and acceptor positions), the differential splicing statistics (DID, pval, padj), the reference exon annotation (donorExon, acceptorExon, skippedExon) and the predicted DID from splice site models (predDIDdonor, predDIDacceptor, when available).

Usage

showOSJ(id, se)

Arguments

id

Character. Orthologous splice junction identifier, i.e. a row name of se (e.g. "ACBD4_3680_3948").

se

SummarizedExperiment. Object returned by annotateOSJ (optionally after runDS and predictDID), whose mcols hold the statistical results and exon annotations.

Value

Invisibly, a list with the values displayed: stats (named vector of DID/pval/padj/significant), annotation (exon columns) and predDID (predicted DID). Called for its side effect of printing a formatted report.

See also

annotateOSJ, runDS, predictDID

Examples

if (FALSE) { # \dontrun{
se <- annotateOSJ(data, se, refSpecies = "Homo_sapiens")
showOSJ("ACBD4_3680_3948", se)
} # }