TsoMergedSmallVariantsGenomeVcfFile R6 Class

Contains methods for reading and displaying contents of the MergedSmallVariants.genome.vcf.gz file output from TSO.

Super class

dracarys::File -> TsoMergedSmallVariantsGenomeVcfFile

Methods

Public methods

• TsoMergedSmallVariantsGenomeVcfFile$read()

• TsoMergedSmallVariantsGenomeVcfFile$write()

• TsoMergedSmallVariantsGenomeVcfFile$clone()

Inherited methods

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

---

Method read()

Reads the MergedSmallVariants.genome.vcf.gz file output from TSO.

Usage

TsoMergedSmallVariantsGenomeVcfFile$read(only_pass = TRUE, alias = TRUE)

Arguments

only_pass

Only include PASS variants (def: TRUE).

alias

Substitute sample names with S1/S2/... alias (def: TRUE).

Returns

tibble with variants.

---

Method write()

Writes a tidy version of the MergedSmallVariants.genome.vcf.gz file output from TSO.

Usage

TsoMergedSmallVariantsGenomeVcfFile$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

TsoMergedSmallVariantsGenomeVcfFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) {
x <- "MergedSmallVariants.genome.vcf.gz"
d <- TsoMergedSmallVariantsGenomeVcfFile$new(x)
d_parsed <- d$read() # or read(d)
d$write(d_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv")
}