SAMultiRunOneCatalog: Run SignatureAnalyzer many times on one catalog and put...

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

Run SignatureAnalyzer many times on one catalog and put results in specified location.

Description

Run SignatureAnalyzer many times on one catalog and put results in specified location.

Usage

SAMultiRunOneCatalog(
  num.runs,
  signatureanalyzer.code.dir,
  input.catalog,
  out.dir,
  maxK = 30,
  tol = 1e-07,
  test.only = FALSE,
  delete.tmp.files = TRUE,
  overwrite = FALSE,
  mc.cores = 1,
  verbose = FALSE,
  seed = NULL
)

Arguments

num.runs	The number of times run SignatureAnalyzer on each catalog (matrix of mutational spectra).
signatureanalyzer.code.dir	The directory holding the SignatureAnalyzer code.
input.catalog	The catalog to analyze.
out.dir	Root of directory tree that will contain the results.
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.
overwrite	If TRUE overwrite previous results in same directory tree.
mc.cores	Number of cores to use for each SignatureAnalyzer run. mclapply; ignored on Windows. The total cores used simultaneously = num.runs * mc.cores.
verbose	If TRUE cat a message regarding progress.
seed	If not NULL call RNGkind(kind = "L'Ecuyer-CMRG"); set.seed(seed).

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