RunmSigActAttributeOnly: Run mSigAct attribution on a spectra catalog file and known...

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

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

Description

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

Usage

RunmSigActAttributeOnly(
  input.catalog,
  gt.sigs.file,
  out.dir,
  CPU.cores = NULL,
  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").
CPU.cores	Number of CPUs to use in running sigfit. For a server, 30 cores would be a good choice; while for a PC, you may only choose 2-4 cores. By default (CPU.cores = NULL), the CPU.cores would be equal to (parallel::detectCores())/2, total number of CPUs divided by 2.
seedNumber	Specify the pseudo-random seed number used to run mSigAct. Setting seed can make the attribution of mSigAct 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 mSigAct, invisibly.

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