CreateFromReal: Create a specific synthetic data set based on real exposures...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Create a specific synthetic data set based on real exposures in one or more cancer types.

Description

Create a full SignatureAnalyzer / SigProfiler test data set for a set of various tumor types.

Usage

CreateFromReal(
  seed,
  top.level.dir = NULL,
  enclosing.dir = NULL,
  num.syn.tumors,
  cancer.types,
  data.suite.name = NULL,
  sa.exp = SynSigGen::sa.all.real.exposures,
  sp.exp = SynSigGen::sp.all.real.exposures,
  overwrite = TRUE,
  regress.dir = NULL,
  unlink = FALSE,
  verbose = FALSE,
  bladder.regress.hack = FALSE
)

Arguments

seed	A random seed to use.
top.level.dir	The directory in which to put the output; will be created if necessary.
enclosing.dir	Deprecated; create the output in a subdirectory of this directory.
num.syn.tumors	The number of tumors to create for each cancer type in cancer.types.
cancer.types	Search sa.exp and sp.exp for exposures from 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.
data.suite.name	Deprecated; the directory created will be file.path(enclosing.dir, paste0(data.suite.name, ".", seed)).
sa.exp	A matrix of exposures; this function will use the columns with column names beginning paste0(cancer.type, "::").
sp.exp	A matrix of exposures; this function will use the columns with column names beginning paste0(cancer.type, "::").
overwrite	If TRUE, overwrite existing directories and files.
regress.dir	If not NULL, compare the result to the contents of this directory with a diff.
unlink	If TRUE and !is.null(regress.dir), then unlink the result directory if there are no differences.
verbose	If TRUE print various informative messages.
bladder.regress.hack	Set this to TRUE to handle mixed "all" and "no hyper" signature sets for the regression test for BladderSkin1000.

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