BestSignatureAnalyzerResult: Find the best SignatureAnalyzer result over a set of output...

In WuyangFF95/SynSigRun: Run Mutational Signature Analysis Software Packages Using Mutational Spectra generated by SynSigGen

Find the best SignatureAnalyzer result over a set of output directories.

Description

Find the best SignatureAnalyzer result over a set of output directories.

Usage

BestSignatureAnalyzerResult(sa.results.dir, verbose = FALSE)

Arguments

sa.results.dir

The directory containing the sa.run.<n> output directories. For example, contents of ../syn.3.5.40.abst.v3/sa.sa.96/sa.results/ must be the directories sa.run.1 sa.run.2 sa.run.3 ... each containing sa.output.other.data.csv sa.output.sigs.csv ... (This function only looks for subdirectories with names of the form sa.run.<n>.) Then #' BestSignatureAnalyzerResult( "../syn.3.5.40.abst.v3/sa.sa.96/sa.results") returns the path to the sa.run.<n> directory with the output from the best SignatureAnalyzer run, e.g. "../syn.3.5.40.abst.v3/sa.sa.96/sa.results/sa.run.3/"

verbose

If TRUE print informative messages to standard output.

Details

As per Jaegil, we first find the most common number of signatures across all the runs, and then among those runs with that number of signatures, we choose the lowest evidence (which is the negative posterior probability).

Value

The path to the directory with the best output as a string, with the list directories examined as the attribute run.directories.

WuyangFF95/SynSigRun documentation built on Oct. 7, 2022, 1:16 p.m.