RunYAPSAAttributeOnly: Run YAPSA attribution on a spectra catalog file and known...

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

Run YAPSA attribution on a spectra catalog file and known signatures.

Description

Run YAPSA attribution on a spectra catalog file and known signatures.

Usage

RunYAPSAAttributeOnly(
  input.catalog,
  gt.sigs.file,
  out.dir,
  seedNumber = 1,
  signature.cutoff = NULL,
  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 YAPSA. Setting seed can make the attribution of YAPSA repeatable. Default: 1.
signature.cutoff	A numeric vector of values less than 1. Signatures from within W with an overall exposure less than the respective value in in_cutoff_vector will be discarded. Default: vector length of number of sigs with all zeros
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 paste0(out.dir, "/sa.output.rdata"). These are TODO(Steve): list the files

Value

The inferred exposure of YAPSA, invisibly.

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