RunSparseSignatures: Run SparseSignatures extraction and attribution on a spectra...

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

Run SparseSignatures extraction and attribution on a spectra catalog file

Description

Run SparseSignatures extraction and attribution on a spectra catalog file

Usage

RunSparseSignatures(
  input.catalog,
  out.dir,
  seedNumber = 1,
  K.exact = NULL,
  K.range = 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").
seedNumber	Specify the pseudo-random seed number used to run SparseSignatures. Setting seed can make the attribution of SparseSignatures repeatable. Default: 1.
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 SparseSignatures 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
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

The inferred exposure of SparseSignatures, invisibly.

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