TsoMsiFile R6 Class

Contains methods for reading and displaying contents of the msi.json.gz file output from TSO.

Super class

dracarys::File -> TsoMsiFile

Methods

Public methods

• TsoMsiFile$read()

• TsoMsiFile$write()

• TsoMsiFile$clone()

Inherited methods

• dracarys::File$bname()
• dracarys::File$initialize()
• dracarys::File$print()
• dracarys::File$type()

---

Method read()

Reads the msi.json.gz file output from TSO.

Usage

TsoMsiFile$read()

Returns

tibble with the following columns:

• label:

---

Method write()

Writes a tidy version of the msi.json.gz file output from TSO.

Usage

TsoMsiFile$write(d, out_dir = NULL, prefix, out_format = "tsv", drid = NULL)

Arguments

d

Parsed object from self$read().

out_dir

Output directory.

prefix

Prefix of output file(s).

out_format

Format of output file(s).

drid

dracarys ID to use for the dataset (e.g. wfrid.123, prid.456).

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TsoMsiFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

x <- system.file("extdata/tso/sample705.msi.json.gz", package = "dracarys")
msi <- TsoMsiFile$new(x)
d_parsed <- msi$read() # or read(msi)
msi$write(d_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv")