VCMetricsFile R6 Class

Contains methods for reading and displaying contents of the vc_metrics.csv file output from DRAGEN, which contains variant calling metrics.

Super class

dracarys::File -> VCMetricsFile

Methods

Public methods

• VCMetricsFile$read()

• VCMetricsFile$write()

• VCMetricsFile$clone()

Inherited methods

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

---

Method read()

Reads the vc_metrics.csv file output from DRAGEN.

Usage

VCMetricsFile$read()

Returns

tibble with one row and metrics spread across individual columns.

---

Method write()

Writes a tidy version of the vc_metrics.csv file output from DRAGEN.

Usage

VCMetricsFile$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

VCMetricsFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

x <- system.file("extdata/wgs/SEQC-II.vc_metrics.csv.gz", package = "dracarys")
vm <- VCMetricsFile$new(x)
d <- vm$read() # or read(vm)
vm$write(d, out_dir = tempdir(), prefix = "seqc_vc", out_format = "tsv")