Runmaftools: Run maftools extraction ONLY on a spectra catalog file

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

Run maftools extraction ONLY on a spectra catalog file

Description

WARNING: maftools can only do signature extraction!

Usage

Runmaftools(
  input.catalog,
  out.dir,
  CPU.cores = NULL,
  K.exact = NULL,
  K.range = NULL,
  nrun.est.K = 10,
  pConstant = 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 maftools. 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 maftools 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. NOTE: Unlike other NMF-based packages, parameter nrun.extract is hard-coded as 1.
pConstant	A small positive value (a.k.a. pseudocount) to add to every entry in the input.catalog. Specify a value ONLY if an "non-conformable arrays error" is raised.
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 extracted signatures of maftools, invisibly.

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