GenSBS1SBS5Exposure: Generate correlated exposures for multiple tumors Wrapper...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Generate correlated exposures for multiple tumors Wrapper function around GenSBS1SBS5ExposureOneTumor: A function to generate exposure of two correlated signatures (Example: SBS1 and SBS5) for sample.number (e.g. 500) synthetic tumors. NOTE: pearson.r.2.lower.thres and pearson.r2.higher.thres are used to constraint the Pearson's R^2 of mutation burdens of two signatures in multiple tumors.

Description

Generate correlated exposures for multiple tumors

Wrapper function around GenSBS1SBS5ExposureOneTumor: A function to generate exposure of two correlated signatures (Example: SBS1 and SBS5) for sample.number (e.g. 500) synthetic tumors.

NOTE: pearson.r.2.lower.thres and pearson.r2.higher.thres are used to constraint the Pearson's R^2 of mutation burdens of two signatures in multiple tumors.

Usage

GenSBS1SBS5Exposure(
  main.signature = "SBS5",
  correlated.signature = "SBS1",
  sample.number = 500,
  name.prefix = "TwoCorreSigsGen",
  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,
  pearson.r.2.lower.thres = 0.1,
  pearson.r.2.higher.thres = 1,
  min.main.to.correlated.ratio.linear = 1/3,
  max.main.to.correlated.ratio.linear = Inf
)

Arguments

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")
sample.number	Number of tumors whose mutation burdens will be generated. (Default: 500)
name.prefix	Prefix of tumor name. (Default: "TwoCorreSigsGen") By default, the name of tumors to be created will be: TwoCorreSigGen::1, TwoCorreSigGen::2, TwoCorreSigGen::3...
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.
pearson.r.2.lower.thres	Minimum Pearson's R^2 of mutation burdens of two signatures in sample.number tumors.
pearson.r.2.higher.thres	Maximum Pearson's R^2 of mutation burdens of two signatures in sample.number tumors.
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.

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