SummarizeOneToolMultiDatasets: Combine results for multiple datasets, from one computational...

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

Combine results for multiple datasets, from one computational approaches.

Description

Summarize results from each computational approach in toolPath/datasetNames and combine them into out.dir.

Usage

SummarizeOneToolMultiDatasets(
  datasetNames = SynSigGen::SBS1SBS5datasetNames,
  datasetGroup,
  datasetGroupName,
  datasetSubGroup = NULL,
  datasetSubGroupName = NULL,
  toolName,
  toolPath,
  out.dir,
  display.datasetName = FALSE,
  overwrite = FALSE
)

Arguments

datasetNames	Names of datasets which are also folder names under toolPath. These folders contain results of toolName on such datasets. E.g. SynSigGen::SBS1SBS5datasetNames
datasetGroup	Numeric or character vector differentiating datasets within each group. E.g. For SBS1-SBS5 correlated datasets, we can consider the value of SBS1-SBS5 exposure ratio as the value for datsetgroup: rep(c(0.1,0.5,1,2,5,10),each = 4) The value is set to Default if unspecified.
datasetGroupName	Meaning of all datasetGroup. E.g. For SBS1-SBS5 correlated datasets, we can consider "SBS1-SBS5 exposure ratio" as what datasetGroup is referring to.
datasetSubGroup	Numeric or character vector differentiating datasets within each sub-group. E.g. For SBS1-SBS5 correlated datasets, we can consider the value of SBS1-SBS5 correlation as the value of subgroup: rep(c(0.1,0.2,0.3,0.6),times = 5)
datasetSubGroupName	Meaning of all datasetSubGroup. E.g. For SBS1-SBS5 correlated datasets, we can consider "SBS1-SBS5 correlation" as what datasetSubGroup is referring to.
toolName	Name of computational approach to be investigated (e.g. "SigProExtractor")
toolPath	The path of the results of the computational approach to be investigated. May include top-level directory (e.g. 3a.Original_output_K_unspecified) and second-level directory containing outputs and summaries of one computational approach to be investigated (e.g. SigProExtractor or SigProExtractor.results). One example: 3a.Original_output_K_unspecified/SigProExtractor Note: this function expects file multiRun.RDa generated by SummarizeMultiRuns under toolPath/datasetNames
out.dir	Path of the output directory.
display.datasetName	Whether to put the name of spectra datasets inside of the csv outputs of summary tables.
overwrite	Whether to overwrite the contents in out.dir if it already exists. (Default: FALSE)

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