SignatureAnalyzer4MatchedCatalogs: Run SignatureAnalyzer on 4 coordinated data sets and put...

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

Run SignatureAnalyzer on 4 coordinated data sets and put results in specified location.

Description

Run SignatureAnalyzer on 4 coordinated data sets and put results in specified location.

Usage

SignatureAnalyzer4MatchedCatalogs(
  num.runs = 20,
  signatureanalyzer.code.dir,
  dir.root,
  maxK = 30,
  tol = 1e-07,
  test.only = FALSE,
  delete.tmp.files = TRUE,
  slice = 1:4,
  overwrite = FALSE,
  mc.cores = 1
)

Arguments

num.runs	Number of SignatureAnalyzer runs per data set.
signatureanalyzer.code.dir	The directory holding the SignatureAnalyzer code.
dir.root	Root of directory tree that contains the input data and to which the results will be written.
maxK	The maximum number of signatures to consider extracting.
tol	Controls when SignatureAnalyzer will terminate its search; tol was 1.e-05 for the PCAWG7 analysis.
test.only	If TRUE, only analyze the first 10 columns read in from input.catalog.
delete.tmp.files	If TRUE delete the many temporary files generated by SignatureAnalyzer.
slice	Vector of integers from 1:4. Only run on the corresponding data set (see Details).
overwrite	if TRUE overwrite preexisting results.
mc.cores	The number of cores to use with mclapply; automatically overridden to 1 on Windows.

Details

The 4 coordinated data sets are

1. sa.sa.96

2. sp.sp

3. sa.sa.COMPOSITE

4. sp.sa.COMPOSITE

which are described elsewhere.

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