ICAMS (version 3.0.11)

ReadCatalogInternal: 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, ID166 (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".