SummarizeSigOneSigProExtractorSubdir: Assess/evaluate results from SigProExtractor (v0.0.5.45+)

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

Assess/evaluate results from SigProExtractor (v0.0.5.45+)

Description

SigProfiler-python de novo extraction and attribution package. Assessment is restricted to v0.0.5.43 ~ v0.0.5.77, because different version has different folder structure.

Usage

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

Arguments

run.dir	A directory which contains output of SigProExtractor in one run on a specific dataset, possibly with a specified seed. E.g. 2b.Full_output_K_as_2/SigProExtractor.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.
hierarchy	Whether the user have enabled hierarchy = True when running SigProExtractor. specifying True or False into SigProExtractor will cause the program to generate different folder structure.
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.

Details

This function cannot be used on new SigProfilerExtractor (v1+) as the folder structure has been changed markedly

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