CreateMixedTumorTypeSyntheticData: Create a test data set based on >= 1 tumor types.

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Create a test data set based on >= 1 tumor types.

Description

Create a test data set based on >= 1 tumor types.

Usage

CreateMixedTumorTypeSyntheticData(
  top.level.dir,
  cancer.type.strings,
  num.syn.tumors,
  overwrite = FALSE,
  sa.exp = sa.all.real.exposures,
  sp.exp = sp.all.real.exposures,
  verbose = FALSE,
  bladder.regress.hack = FALSE
)

Arguments

top.level.dir	Path to top level of directory structure to be created.
cancer.type.strings	Search the PCAWG data for tumors matching these strings. Each string should identify one tumor type, for some definition of tumor type. Probably the tumors in each type should be non-overlapping, but the code does not enforce this and does not care.
num.syn.tumors	Number of synthetic tumors to create for each cancer type.
overwrite	If TRUE, overwrite existing directories / files.
sa.exp	SignatureAnalyzer exposures from which to select cancer types specified by cancer.type.strings. In the column names of sa.exp the cancer type string should be separated from the sample identifier by two colons (::).
sp.exp	SigProfiler exposures from which to select cancer types specified by cancer.type.strings. In the column names of sp.exp the cancer type string should be separated from the sample identifier by two colons (::).
verbose	If > 0, cat various messages.
bladder.regress.hack	For use by BladderSkin1000. Forces use of non-hyper-mutated exposures for bladder-TCC even if sa.exp and sp.exp include hyper-mutated exposures.

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