ConvertCatalogToSigProfilerFormat: Covert an ICAMS Catalog to SigProfiler format

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Covert an ICAMS Catalog to SigProfiler format

Description

Specially, the row orders in ICAMS internal format (see ICAMS::catalog.row.order) are converted to headers in SigProfiler format.

Usage

ConvertCatalogToSigProfilerFormat(input.catalog, file, sep = "\t")

Arguments

input.catalog	Either a character string, in which case this is the path to a file containing a catalog in ICAMS format, or an in-memory ICAMS catalog.
file	The path of the file to be written.
sep	Separator to use in the output file.

Details

For SigProfiler formats, please see the links below for:

• SBS: https://osf.io/s93d5/wiki/5.%20Output%20-%20SBS/

• DBS: https://osf.io/s93d5/wiki/5.%20Output%20-%20DBS/

• ID: https://osf.io/s93d5/wiki/5.%20Output%20-%20ID/

Note

This function can only transform SBS96, SBS192, SBS1536, DBS78 and ID ICAMS catalog to SigProfiler format.

Examples

path <- system.file("extdata",
                    "strelka.regress.cat.sbs.96.csv",
                    package = "ICAMS")
catSBS96 <- ReadCatalog(path)
ConvertCatalogToSigProfilerFormat(input.catalog = catSBS96,
                                  file = file.path(tempdir(), "sigproCat.txt"))

ICAMS documentation built on June 15, 2025, 1:08 a.m.