Create.3.5.40.Abstract: Create synthetic spectra based on SBS3 SBS5 SBS40

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Create synthetic spectra based on SBS3 SBS5 SBS40

Description

This function generates synthetic spectra with mutation loads of SBS3 (signature prevalent in ovarian adenocarcinoma), SBS5 and SBS40 (signatures prevalent in renal cell carcinoma). This dataset challenges the computational approaches as these three signatures are "flat" signatures hard to be extracted accurately.

Usage

Create.3.5.40.Abstract(
  seed = 44,
  overwrite = TRUE,
  regress.dir = "data-raw/long.test.regression.data/syn.3.5.40.abst/",
  num.syn.tumors = 1000,
  top.level.dir = paste0("../syn.3.5.40.abst.", seed),
  unlink = FALSE
)

Arguments

seed	A random seed to use.
overwrite	If TRUE, overwrite existing directories / files.
regress.dir	If not NULL, compare the result to the contents of this directory with a diff.
num.syn.tumors	The number of tumors to create for each cancer type in cancer.types.
top.level.dir	The directory in which to put the output; will be created if necessary.
unlink	If TRUE and !is.null(regress.dir), then unlink the result directory if there are no differences.

Details

This function supersedes the second part of data-raw/Create.3.5.40.Rmd in GitHub repository steverozen/SynSig. With default arguments, this function generates the same results as the second half of data-raw/Create.3.5.40.Rmd.

Data set generated by this function can be found at Synapse with Synapse ID: syn18500215.

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