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TsoTmbFile R6 Class

Source: R/tso.R
TsoTmbFile.Rd

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

Super class

dracarys::File -> TsoTmbFile

Methods

Public methods

Inherited methods

Method read()

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

Usage

TsoTmbFile$read()

Returns

tibble with the following columns:

  • TmbPerMb

  • AdjustedTmbPerMb

  • NonsynonymousTmbPerMb

  • AdjustedNonsynonymousTmbPerMb

  • SomaticCodingVariantsCount

  • NonsynonymousSomaticCodingVariantsCount

  • TotalRegionSizeMb

  • CodingRegionSizeMb

Method write()

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

Usage

TsoTmbFile$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

TsoTmbFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

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