RCCOvary1000: Create synthetic spectra based on renal cell carcinoma and...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Create synthetic spectra based on renal cell carcinoma and ovarian adenocarcinoma

Description

Creates spectra dataset consists of 500 synthetic renal cell carcinoma (RCC) with high prevalence and mutation load from SBS5 and SBS40 signatures, and 500 synthetic ovarian adenocarcinoma with high prevalence and mutation load from SBS3. This dataset challenges the computational approaches as these three signatures are "flat" signatures hard to be extracted accurately.

Usage

RCCOvary1000(
  seed = 191905,
  unlink = FALSE,
  regress.dir = NULL,
  top.level.dir = "tmp.3.5.40.RCC.and.ovary"
)

Arguments

seed	A random seed to use.
unlink	The directory in which to put the output; will be created if necessary.
regress.dir	If not NULL, compare the result to the contents of this directory with a diff.
top.level.dir	The directory in which to put the output; will be created if necessary.

Details

This function Replaces the first 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 first part of data-raw/Create.3.5.40.Rmd.

The second half of data-raw/Create.3.5.40.Rmd in steverozen/SynSig is replaced by Create.3.5.40.Abstract.

Data set generated by this function can be found at Synapse with Synapse ID: syn18500214.

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