PcgrTiersFile R6 Class

Contains methods for reading and displaying contents of the pcgr.snvs_indels.tiers.tsv file output from PCGR.

Super class

dracarys::File -> PcgrTiersFile

Methods

Public methods

• PcgrTiersFile$read()

• PcgrTiersFile$write()

• PcgrTiersFile$clone()

Inherited methods

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

---

Method read()

Reads the pcgr.snvs_indels.tiers.tsv file output from PCGR.

Usage

PcgrTiersFile$read()

Returns

List of tibbles.

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Method write()

Writes a tidy version of the pcgr.snvs_indels.tiers.tsv file output from PCGR.

Usage

PcgrTiersFile$write(d, out_dir, prefix, out_format = "tsv")

Arguments

d

Parsed object from self$read().

out_dir

Output directory.

prefix

Prefix of output file(s).

out_format

Format of output file(s) (one of 'tsv' (def.), 'parquet', 'both').

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Method clone()

The objects of this class are cloneable with this method.

Usage

PcgrTiersFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) {
x <- "/path/to/pcgr.snvs_indels.tiers.tsv"
d <- PcgrTiersFile$new(x)
d_parsed <- d$read() # or read(d)
d$write(d_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "both")
}