Runtcsm: Run tcsm extraction and attribution on a spectra catalog file

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

Run tcsm extraction and attribution on a spectra catalog file

Description

Run tcsm extraction and attribution on a spectra catalog file

Usage

Runtcsm(
  input.catalog,
  out.dir,
  seedNumber = 1,
  CPU.cores = 1,
  K.exact = NULL,
  K.range = NULL,
  covariates = NULL,
  test.only = FALSE,
  overwrite = FALSE,
  feature.file = NULL,
  effect.output.file = NULL,
  sigma.output.file = NULL,
  gamma.output.file = NULL
)

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").
seedNumber	Specify the pseudo-random seed number used to run tcsm. Setting seed can make the attribution of tcsm repeatable.
CPU.cores	Number of CPUs to use in running MutationalPatterns. 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.
K.exact, K.range	K.exact is the exact value for the number of signatures active in spectra (K). Specify K.exact if you know exact how many signatures are active in the input.catalog, which is the ICAMS-formatted spectra file. K.range is A numeric vector (K.min,K.max) of length 2 which tell tcsm to search the best signature number active in spectra, K, in this range of Ks. Specify K.range if you don't know how many signatures are active in the input.catalog. K.max - K.min >= 3, otherwise an error will be thrown. WARNING: You must specify only one of K or K.range!
test.only	If TRUE, only analyze the first 10 columns read in from input.catalog.
overwrite	If TRUE, overwrite existing output.

Details

Creates several files in out.dir. These are: TODO(Steve): list the files

TODO(Wuyang)

Value

The inferred exposure of tcsm, invisibly.

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