SummarizeSigOneSigProSSSubdir: Assess/evaluate results from sigproSS (a.k.a. SigProfiler...

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

Assess/evaluate results from sigproSS (a.k.a. SigProfiler Python attribution package)

Description

Assess/evaluate results from sigproSS (a.k.a. SigProfiler Python attribution package)

Usage

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

Arguments

run.dir	Lowest level path to results, e.g. <top.dir>/sa.sa.96/ExtrAttr/SigProExtractor.results/seed.1/ 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. However there should be a directory <run.dir>/SBS96 which stores SigProfiler results.
ground.truth.exposure.dir	TODO(Wu Yang): Fix this File name which stores ground-truth exposures; defaults to "ground.truth.syn.exposures.csv". This file can be found in the sub.dir, i.e. <run.dir>/../../../
overwrite	If TRUE overwrite existing directories and files.
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.