RunSignatureEstimationQPAttributeOnly: Run SignatureEstimation Quadratic Programming (QP)...

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

Run SignatureEstimation Quadratic Programming (QP) attribution on a spectra catalog file and known signatures.

Description

Run SignatureEstimation Quadratic Programming (QP) attribution on a spectra catalog file and known signatures.

Usage

RunSignatureEstimationQPAttributeOnly(
  input.catalog,
  gt.sigs.file,
  out.dir,
  seedNumber = 1,
  test.only = FALSE,
  overwrite = FALSE
)

Arguments

input.catalog	File containing input spectra catalog. Columns are samples (tumors), rows are mutation types.
gt.sigs.file	File containing input mutational signatures. Columns are signatures, 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 SignatureEstimation. Setting seed can make the attribution of SignatureEstimation repeatable. Default: 1.
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

Value

Invisibly returns a list which contains:

• $exposuresCounts: the exposure counts inferred in ICAMSxtra format,

• $exposureErrors: the MSE in ICAMSxtra format,

• $SEoutput: A list which contains:

  • $exposures: exposure proportion in SignatureEstimation format, and errors invisibly.

  • $errors: mean squared error (MSE) between normalized reconstructed spectra and normalized ground-truth mutational spectra.

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