RunMutationalPatterns: Run MutationalPatterns extraction and attribution on a...

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

Run MutationalPatterns extraction and attribution on a spectra catalog file

Description

WARNING: MutationalPatterns can only do exposure attribution using SBS96 spectra catalog and signature catalog!

Usage

RunMutationalPatterns(
  input.catalog,
  out.dir,
  CPU.cores = NULL,
  K.exact = NULL,
  K.range = NULL,
  nrun.est.K = 10,
  nrun.extract = 200,
  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 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 exactly 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 MutationalPatterns 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. WARNING: You must specify only one of K.exact or K.range! Default: NULL
nrun.est.K	Number of NMF runs for each possible number of signature. This is used in the step to estimate the most plausible number of signatures in input spectra catalog.
nrun.extract	number of NMF runs for extracting signatures and inferring exposures.
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)

NOTE: The seed is hard-coded in MutationalPatterns as 123456.

pConstant is harded-coded as 1e-04.

Value

A list contains:

• $signature extracted signatures,

• $exposure inferred exposures,

of MutationalPatterns, invisibly.

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