SummarizeSigOneAttrSubdir: Assess/evaluate results from packages which can ONLY do...

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

Assess/evaluate results from packages which can ONLY do exposure attribution.

Description

Packages including but not limited to: deconstructSigs, YAPSA.

Usage

SummarizeSigOneAttrSubdir(
  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/Attr/YAPSA.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. For packages which can do both extraction and attribution, we expect two files, reference.signatures.csv and inferred.exposures.csv are in the folder.
ground.truth.exposure.dir	Folder which stores ground-truth exposures. It defaults to be 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.

Details

Here, we excluded SignatureEstimation. Although it is also a package with only attribution, but it has two attribution algorithms. Therefore the naming of the results are slightly different from the other two packages.

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