SAAndSPSynDataOneCAType: Generate parallel synthetic exposures from real SA and SP...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Generate parallel synthetic exposures from real SA and SP exposures and signatures

Description

Generate parallel synthetic exposures from real SA and SP exposures and signatures

Usage

SAAndSPSynDataOneCAType(
  sa.real.exp,
  sp.real.exp,
  ca.type,
  num.syn.tumors,
  file.prefix,
  top.level.dir = NULL
)

Arguments

sa.real.exp	Exposure matrix from SignatureAnalyzer.
sp.real.exp	Exposure matrix from SigProfiler.
ca.type	The type the cancer, which is used in sample identifiers, which SigProfiler expects.
num.syn.tumors	Number of synthetic tumors to generate.
file.prefix	To explain later.
top.level.dir	Specifies the location to generate files.

Value

A list with the following elements:

1. sa.parms The parameters computed from sa.real.exp. This a matrix with a column for each signature and 3 rows:

   1. The proportion of tumors with given signature (in sa.real.exp).

   2. The mean of the log10 of the number of mutations for a given signature.

   3. The standard deviation of log10 of the number of mutations for a given signature.

2. sa.syn.exp The synthetic exposures computed from sa.parms.

3. sp.parms The parameters computed from sp.real.exp, with rows analogous to the rows in sa.parms.

4. sp.syn.exp The synthetic exposures computed from sp.parms.

@details Creates a bunch of files in location governed by top.level.dir. The main rationale for packaging this as one function is to ensure that some conventions regarding file naming are followed.

This function does not create the synthetic mutational spectra catalogs but does generate the synthetic exposures.

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