RunMutationalPatternsAttributeOnly: Run MutationalPatterns attribution on a spectra catalog file...

In WuyangFF95/SynSigRun: Run Mutational Signature Analysis Software Packages Using Mutational Spectra generated by SynSigGen

Run MutationalPatterns attribution on a spectra catalog file and known signatures.

Description

Run MutationalPatterns attribution on a spectra catalog file and known signatures.

Usage

RunMutationalPatternsAttributeOnly(
  input.catalog,
  gt.sigs.file,
  out.dir,
  seedNumber = 1,
  test.only = FALSE,
  overwrite = FALSE
)

Arguments

input.catalog	File containing input spectra catalog. Columns are samples (tumors), rows are mutation types.
gt.sigs.file	File containing input mutational signatures. Columns are signatures, rows are mutation types.
out.dir	Directory that will be created for the output; abort if it already exits. Log files will be in paste0(out.dir, "/tmp").
seedNumber	Specify the pseudo-random seed number used to run MutationalPatterns. Setting seed can make the attribution of MutationalPatterns repeatable. Default: 1.
test.only	If TRUE, only analyze the first 10 columns read in from input.catalog. Default: FALSE
overwrite	If TRUE, overwrite existing output. Default: FALSE

Details

Creates several files in paste0(out.dir, "/sa.output.rdata"). These are TODO(Steve): list the files

Value

The inferred exposure of MutationalPatterns, invisibly.

WuyangFF95/SynSigRun documentation built on Oct. 7, 2022, 1:16 p.m.