TsoCombinedVariantOutputFile R6 Class

Contains methods for reading and displaying contents of the CombinedVariantOutput.tsv file output from TSO.

Super class

dracarys::File -> TsoCombinedVariantOutputFile

Methods

Public methods

• TsoCombinedVariantOutputFile$read()

• TsoCombinedVariantOutputFile$write()

• TsoCombinedVariantOutputFile$clone()

Inherited methods

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

---

Method read()

Reads the CombinedVariantOutput.tsv file output from TSO and extracts only the Small Variants section (due to inconsistencies with other sections).

Usage

TsoCombinedVariantOutputFile$read()

Returns

tibble with variants.

---

Method write()

Writes a tidy version of the CombinedVariantOutput.tsv (only Small Variants) file output from TSO.

Usage

TsoCombinedVariantOutputFile$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

TsoCombinedVariantOutputFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) {
x <- "/path/to/CombinedVariantOutput.tsv"
d <- TsoCombinedVariantOutputFile$new(x)
d$read()
}