SummarizeSigOneExtrAttrSubdir: Assess/evaluate results from packages which can do BOTH...

In WuyangFF95/SynSigEval: Evaluate Results of Mutational Signature Analysis Software on Synthetic Spectra Created by Package SynSigGen

Assess/evaluate results from packages which can do BOTH extraction and attribution, excluding SigProfiler-Python and SignatureAnalyzer.

Description

Packages including but not limited to: hdp, MutationalPatterns, sigfit, signeR, SomaticSignatures.

Usage

SummarizeSigOneExtrAttrSubdir(
  run.dir,
  ground.truth.exposure.dir = paste0(run.dir, "/../../../"),
  summarize.exp = TRUE,
  overwrite = FALSE,
  summary.folder.name = "summary",
  export.Manhattan.each.spectrum = FALSE
)

Arguments

run.dir	A directory which contains output of computational approach in one run on a specific dataset, possibly with a specified seed. E.g. 2b.Full_output_K_as_2/hdp.results/S.0.1.Rsq.0.1/seed.1/. This code depends on a conventional directory structure documented in NEWS.md.
ground.truth.exposure.dir	Folder which stores ground-truth exposures. Should contain a file named ground.truth.syn.exposures.csv. In PCAWG paper: run.dir/../../ In SBS1-SBS5 paper: 0.Input_datasets/S.0.1.Rsq.0.1/
summarize.exp	Whether to summarize exposures when the file specified by inferred.exp.path exists.
overwrite	If TRUE overwrite and files in existing run.dir/summary folder.
summary.folder.name	The name of the folder containing summary results. Usually, it equals to "summary".
export.Manhattan.each.spectrum	Whether to export csv files for Manhattan distance of each mutational spectrum.

WuyangFF95/SynSigEval documentation built on Sept. 18, 2022, 11:41 a.m.