Runsigminer: Run sigminer extraction and attribution on a spectra catalog...

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

Run sigminer extraction and attribution on a spectra catalog file

Description

Run sigminer extraction and attribution on a spectra catalog file

Usage

Runsigminer(
  input.catalog,
  out.dir,
  CPU.cores = NULL,
  seedNumber = 1,
  K.max = NULL,
  test.only = FALSE,
  overwrite = FALSE
)

Arguments

input.catalog	File containing input spectra catalog. Columns are samples (tumors), 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 sigminer. 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 SomaticSignatures. Setting seed can make the attribution of SomaticSignatures repeatable. Default: 1.
K.max	K.max is the maximum number of signatures users expect to active in input.catalog. As this approach cannot specify K.exact, you can specify K.max = K.exact If you know exactly how many signatures are active in the input.catalog. On the other hand, you may specify max(K.range) if you don't know how many signatures are active in the input.catalog.
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 out.dir. These are: TODO(Steve): list the files

TODO(Wuyang)

Value

A list contains:

• $signature extracted signatures,

• $exposure inferred exposures,

of sigminer, invisibly.

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