ReadCatalog {ICAMS}

Read catalog

Description

Read a catalog in standardized format from path.

Usage

ReadCatalog(
  file,
  ref.genome = NULL,
  region = "unknown",
  catalog.type = "counts",
  strict = NULL,
  stop.on.error = TRUE
)

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".

strict

Ignored and deprecated.

stop.on.error

If TRUE, call stop on error; otherwise return a 1-column matrix of NA's with the attribute "error" containing error information. The number of rows may not be the correct number for the expected catalog type.

Details

See also WriteCatalog

Value

A catalog as an S3 object; see as.catalog.

Comments

To add or change attributes of the catalog, you can use function attr.
For example, attr(catalog, "abundance") <- custom.abundance.

Note

In ID (small insertion and deletion) catalogs, deletion repeat sizes range from 0 to 5+, but for plotting and end-user documentation deletion repeat sizes range from 1 to 6+.

Examples

file <- system.file("extdata",
                    "strelka.regress.cat.sbs.96.csv",
                    package = "ICAMS")
catSBS96 <- ReadCatalog(file)