ICAMS (version 2.1.2)

ReadCatalog: Read catalog.

Description

Read a catalog in standardized format from path.

Usage

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

Arguments

file

Path to a catalog on disk in the standardized format.

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

If TRUE, do additional checks on the input, and stop if the checks fail.

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.

Details

See also WriteCatalog

Examples

# NOT RUN {
file <- system.file("extdata",
                    "strelka.regress.cat.sbs.96.csv",
                    package = "ICAMS")
catSBS96 <- ReadCatalog(file)
# }