CreatehelmsmanOutput: Prepare input file for helmsman from a helmsman formatted...

In WuyangFF95/SynSigEval: Evaluate Results of Mutational Signature Analysis Software on Synthetic Spectra Created by Package SynSigGen

Prepare input file for helmsman from a helmsman formatted catalog file.

Description

Prepare input file for helmsman from a helmsman formatted catalog file.

Usage

CreatehelmsmanOutput(
  catalog,
  out.dir = paste0(dirname(catalog), "/ExtrAttr/helmsman.results"),
  overwrite = FALSE
)

Arguments

catalog	a catalog in ICAMS format. It can be a .csv file, or a matrix or data.frame. Usually, it refers to "ground.truth.syn.catalog.csv".
out.dir	Directory that will be created for the output; abort if it already exists. Usually, the out.dir will be a helmsman.results folder directly under the folder storing catalog.
overwrite	If TRUE, overwrite existing output

Details

Creates folder named helmsman.results containing catalogs in helmsman-formatted catalogs: Rows are signatures; the first column is the name of the mutation type, while the remaining columns are samples (tumors). These helmsman-formatted catalogs will the input when running helmsman program later on Python platform.

Value

invisible(catMatrix), original catalog in helmsman format

WuyangFF95/SynSigEval documentation built on Sept. 18, 2022, 11:41 a.m.