ReadCatalogInternal: Internal read catalog function to be wrapped in a tryCatch

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

Internal read catalog function to be wrapped in a tryCatch

Description

Internal read catalog function to be wrapped in a tryCatch

Usage

ReadCatalogInternal(
  file,
  ref.genome = NULL,
  region = "unknown",
  catalog.type = "counts"
)

Arguments

file	Path to a catalog on disk in a standardized format. The recognized formats are: ICAMS formatted SBS96, SBS192, SBS1536, DBS78, DBS136, DBS144, ID (see CatalogRowOrder). SigProfiler-formatted SBS96, DBS78 and ID83 catalogs; see https://github.com/AlexandrovLab/SigProfilerExtractor. COSMIC-formatted SBS96, SBS192 (a.k.a. TSB192), DBS78, ID83 catalogs; see https://cancer.sanger.ac.uk/signatures/.
ref.genome	A ref.genome argument as described in ICAMS.
region	region A character string designating a genomic region; see as.catalog and ICAMS.
catalog.type	One of "counts", "density", "counts.signature", "density.signature".

ICAMS documentation built on June 22, 2024, 6:47 p.m.