ReadID115Catalog: Read catalog

In steverozen/ICAMSxtra: ICAMSxtra

Description

Read a catalog in standardized format from path.

Usage

ReadID115Catalog(
  file,
  ref.genome = NULL,
  region = "unknown",
  catalog.type = "counts"
)

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".

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+.

steverozen/ICAMSxtra documentation built on Feb. 9, 2022, 7:01 a.m.