SummarizeSigOneSASubdir: Summarize results (SBS96, DBS, ID or COMPOSITE) from...

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

Summarize results (SBS96, DBS, ID or COMPOSITE) from SignatureAnalyzer

Description

Summarize results (SBS96, DBS, ID or COMPOSITE) from SignatureAnalyzer

Usage

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

Arguments

run.dir	Lowest level path to results, for example in PCAWG paper: <top.dir>/sa.sa.96/sa.results/, <top.dir>/sp.sp/sa.results/, <top.dir>/sa.sa.COMPOSITE/sa.results/, or <top.dir>/sp.sa.COMPOSITE/sa.results/. In SBS1-SBS5 paper: 2b.Full_output_K_as_2/SignatureAnalyzer.results/S.0.1.Rsq.0.1/seed.1/ We expect run.dir contain the best-run subdirectory (e.g. "best.run"). The name of the subdirectory needs to be given to which.run parameter. Here, <top.dir> refers to a top-level directory which contains the full information of a synthetic dataset. (e.g. syn.2.7a.7b.abst.v8) This code depends on a conventional directory structure documented elsewhere.
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/
which.run	Name of subdirectory under run.dir containing the run to summarize.
summarize.exp	Whether to summarize exposures when the <run.dir>/<which.run>/sa.output.exp.csv 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.