SignatureAnalyzerPrepHyper1Secondary: Prepare the "hypermutated" segment (a.k.a "Secondary" segment...

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

Prepare the "hypermutated" segment (a.k.a "Secondary" segment of a split non-hyper and hyper data set.)

Description

Prepare the "hypermutated" segment (a.k.a "Secondary" segment of a split non-hyper and hyper data set.)

Usage

SignatureAnalyzerPrepHyper1Secondary(
  non.hyper.results,
  primary.catalog,
  hyper.catalog,
  secondary.catalog,
  overwrite = TRUE
)

Arguments

non.hyper.results	The directory containing the the results of the analysis of the non-hyper-mutated (a.k.a "PRIMARY") mutational spectra.
primary.catalog	The catalog of non-hyper-mutated mutational spectra from which the results in non.hyper.results were derived.
hyper.catalog	The catalog of hyper-mutated mutational spectra which will be part of the input for the secondary analysis.
secondary.catalog	The final output catalog on which the secondary analysis will be performed; this is a cbind of pseudo-spectra generated from the PRIMARY signatures with the hyper.catalog.
overwrite	If TRUE overwrite possible previously computed files and/or directories.

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