RunSignatureAnalyzerAttribution: Run SignatureAnalyzer attribution on a catalog file and...

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

Run SignatureAnalyzer attribution on a catalog file and output by RunSignatureAnalyzerOnFile().

Description

Normally, please call SignatureAnalyzerOneRun instead of this function.

Usage

RunSignatureAnalyzerAttribution(
  input.catalog,
  read.catalog.function,
  extracted.signature.file,
  raw.exposures.file,
  write.signature.function,
  out.dir,
  test.only = FALSE,
  input.exposures = NULL,
  delete.tmp.files = TRUE,
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

input.catalog	File containing input catalog. Columns are samples (tumors), rows are signatures. SignatureAnalyzer does not care about the row names (I think) TODO(Steve): check this.
read.catalog.function	Function taking a file path as its only argument and returning a catalog as a numeric matrix.
extracted.signature.file	A .csv file containing extracted signatures. Normally, this file is named "sa.output.sigs.csv" and is generated by function RunSignatureAnalyzerOnFile(). It expects to have the same format as the input.catalog, thus it will be read by read.catalog.function too.
raw.exposures.file	A .csv file containing raw attributions of exposures. Normally, this file is named "sa.output.raw.exp.csv" and is generated by function RunSignatureAnalyzerOnFile().
write.signature.function	Function with first argument the signatures generated by SignatureAnalyzer and second argument the file to write to.
out.dir	Directory that will be created for the output; abort if it already exits. Log files will be in paste0(out.dir, "/tmp").
test.only	If TRUE, only analyze the first 10 columns read in from input.catalog.
input.exposures	A file with the synthetic exposures used to generate input.catalog; if provided here, this is copied over to the output directory for downstream analysis.
delete.tmp.files	If TRUE delete the many temporary files generated by SignatureAnalyzer.
overwrite	If TRUE, overwrite existing output.
verbose	If TRUE cat a message regarding progress.

Details

Save the final attribution of a catalog matrix into a file named "sa.output.fine.exp.csv" under the folder out.dir.

Value

The final attribution matrix. (i.e. exp.fine.tuned)

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