CreateSBS1SBS5CorrelatedSyntheticData: Function to generate 20 SBS1-SBS5-correlated Synthetic...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Function to generate 20 SBS1-SBS5-correlated Synthetic datasets used in testing.

Description

This function is a wrapper around CreateSBS1SBS5CorrelatedSyntheticDataOneDataset. It will use the default parameters to repeat the results.

Usage

CreateSBS1SBS5CorrelatedSyntheticData(
  top.level.dir = "./",
  regress.dir = NULL,
  overwrite = FALSE,
  add.info = TRUE,
  unlink = FALSE
)

Arguments

top.level.dir	Top-level-folder to place 20 spectra datasets generated by this function. Default: ./ (Current working directory)
regress.dir	If not NULL, compare the result to the contents of this directory with a diff.
overwrite	Whether to overwrite (Default: FALSE)
add.info	Whether to generate additional information. You should set it to FALSE when you want to make a diff (i.e. regressdir is not NULL). This is because Additional information may differ on different OS or R sessions, thus may prevent the dataset from passing the NewDiff4SynDatasets check. (Default: TRUE)
unlink	Whether to delete temporary dataset folder top.level.dir. (Set to TRUE for testing)

Details

This function will generate 20 datasets, each with files listed below:

ground.truth.syn.catalog.csv: Generated tumor spectra in ICAMS SBS96 CSV format.

ground.truth.syn.exposures.csv: Mutation burdens of SBS1 and SBS5 in generated tumor spectra in ICAMS CSV format.

ground.truth.syn.sigs.csv: Ground-truth SBS1 and SBS5 signatures in ICAMS SBS96 CSV format.

parameters.txt: Parameters used to generate the exposures and tumor spectra.

scatterplot.pdf: scatterplot illustrating correlation of exposures of two signatures in generated spectra

seedInUse.txt, RNGInUse.txt: seed and Random Number Generator used in generation. (For better reproducibility)

sessionInfo.txt: information related to R versions, platforms, loaded or imported packages, etc. (For better reproducibility)

steverozen/SynSigGen documentation built on April 1, 2022, 8:54 p.m.