SummarizeSigOneSubdir: Assess/evaluate one result sub-folder from a computational...

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

Assess/evaluate one result sub-folder from a computational approach

Description

Note: For summarizing SigProExtractor or SignatureAnalyzer, users should use SigProExtractor(SigProfiler-Python) v0.0.5.43+ and SignatureAnalyzer 2018-Apr-18.

Usage

SummarizeSigOneSubdir(
  run.dir,
  ground.truth.exposure.dir,
  extracted.sigs.path,
  inferred.exp.path = NULL,
  summarize.exp = TRUE,
  overwrite = FALSE,
  summary.folder.name = "summary",
  export.Manhattan.each.spectrum = FALSE,
  verbose = 0
)

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/
extracted.sigs.path	Path to extracted sigs file. For most computational approaches, it's in: <run.dir>/extracted.signatures.csv. For SigProExtractor, it's in: <run.dir>/<catalog.type>/Selected_Solution/De_Novo_Solution/De_Novo_Solution_Signatures_<catalog.type>.txt , and is converted to <run.dir>/extracted.signatures.csv by wrapper function SummarizeSigProExtractor. For SignatureAnalyzer, it's in: <run.dir>/sa.output.sigs.csv For EMu, helmsman.NMF, MultiModalMuSig.LDA and MultiModalMuSig.CTM, their extracted signature files are not standard ICAMS catalog format. These non-standard extracted signatures are converted to extracted.signatures.csv, a standard ICAMS catalog by their respective wrapper functions: ReadEMuCatalog, helmsmanCatalog2ICAMS, and MMCatalog2ICAMS They are dumped into extracted.sigs.csv same as most approaches.
inferred.exp.path	Path to inferred exposures file. For most computational approaches, it's in: <run.dir>/inferred.exposures.csv. For SigProExtractor, it's in <run.dir>/<catalog.type>/Selected_Solution/De_Novo_Solution/De_Novo_Solution_Activities_<catalog.type>.txt , and is converted to <run.dir>/inferred.exposures.csv by wrapper function SummarizeSigProExtractor. For SignatureAnalyzer, it's in: <run.dir>/sa.output.exp.csv For EMu, helmsman.NMF, MultiModalMuSig.LDA and MultiModalMuSig.CTM, their extracted signature files are not standard ICAMS catalog format. These non-standard extracted signatures are converted to extracted.signatures.csv, a standard mSigTools exposures by their respective wrapper functions: ReadEMuExposureFile ReadhelmsmanExposure, and ReadExposureMM They are dumped into inferred.exposures.csv same as most approaches.
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.
verbose	If > 0, print progress / checking messages.

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