GenSBS1SBS5ExposureOneTumor: Generate correlated exposures for one tumor Function to...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Generate correlated exposures for one tumor Function to generate exposure of two correlated signatures (Example: SBS1 and SBS5) for ONE synthetic tumor.

Description

Generate correlated exposures for one tumor

Function to generate exposure of two correlated signatures (Example: SBS1 and SBS5) for ONE synthetic tumor.

Usage

GenSBS1SBS5ExposureOneTumor(
  tumor.name = "TwoCorreSigsGen::1",
  main.signature = "SBS5",
  correlated.signature = "SBS1",
  main.mean.log = 2.5,
  main.stdev.log = 0.25,
  correlated.stdev.log = 0.25,
  slope.linear = 1,
  main.signature.lower.thres = 50,
  correlated.signature.lower.thres = 30,
  min.main.to.correlated.ratio.linear = 1/3,
  max.main.to.correlated.ratio.linear = Inf
)

Arguments

tumor.name	Name of synthetic tumor you want to generate. (default: TwoCorreSigsGen::1)
main.signature	Name of a signature with smaller variance in the log10 space. (default: "SBS5")
correlated.signature	Name of a signature with larger variance in the log10 space. (default: "SBS1")
main.mean.log	Mean of log10(mutation burden of main.signature)
main.stdev.log	Standard deviation of log10(mutation burden of main.signature)
correlated.stdev.log	Contribute to part of the standard deviation of log10(mutation burden of correlated.signature). In this script, the s.d. of log10(mutation burden of correlated.signature) = main.stdev.log + correlated.stdev.log
slope.linear	Average ratio of mutation burden of correlated.signature over mutation burden of main.signature
main.signature.lower.thres	Minimum mutation burden (number of mutations) induced by main.signature in each tumor.
correlated.signature.lower.thres	Minimum mutation burden (number of mutations) induced by correlated.signature in each tumor.
min.main.to.correlated.ratio.linear	Minimum ratio of main.signature over mutation burden of correlated.signature in each tumor.
max.main.to.correlated.ratio.linear	Maximum ratio of main.signature over mutation burden of correlated.signature in each tumor.

Warning Warning 1

forcing dataset to have high Pearson's R^2, while inputting large main.stdev.log value will cause the program to reject unqualified datasets and regenerate new datasets for HOURS OR EVEN DAYS.

Warning 2: If users intend to replicate results of SBS1-SBS5 paper, please specify parameters as indicated in the Supplementary Information of the paper.

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