Export a catalog or signature set in a file format

Writes the channel x column matrix of an [MsCatalog] (counts) or [MsSignature] (probabilities) in the requested format. The first interop format is `cosmic` (the bundled COSMIC v3.6 file layout: TSV, "Type" first header column, one row per channel label in canonical registry order).

Usage

ms_export(x, format = "cosmic", file = NULL)

Arguments

x

An [MsCatalog] or [MsSignature].

format

`"cosmic"` (the bundled reference layout, first header column "Type") or `"sigprofiler"` (first header column "MutationType"; verified against upstream specimens – memo section 4). WTSI long format is deferred (no verifiable upstream specimen).

file

Output path; `NULL` returns the assembled data.frame instead of writing.

Value

The data.frame (file = NULL) or the file path, invisibly.