WgsCoverageMetricsFile R6 Class

Contains methods for reading and displaying contents of the wgs_coverage_metrics_<phenotype>.csv file output from DRAGEN. This file contains read depth of coverage metrics.

Super class

dracarys::File -> WgsCoverageMetricsFile

Methods

Public methods

• WgsCoverageMetricsFile$read()

• WgsCoverageMetricsFile$write()

• WgsCoverageMetricsFile$clone()

Inherited methods

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

---

Method read()

Reads the wgs_coverage_metrics_<phenotype>.csv file output from DRAGEN.

Usage

WgsCoverageMetricsFile$read()

Returns

tibble with one row and metrics spread across individual columns.

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Method write()

Writes a tidy version of the wgs_coverage_metrics_<phenotype>.csv file output from DRAGEN

Usage

WgsCoverageMetricsFile$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).

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Method clone()

The objects of this class are cloneable with this method.

Usage

WgsCoverageMetricsFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

x1 <- system.file("extdata/wgs/SEQC-II.wgs_coverage_metrics_normal.csv.gz", package = "dracarys")
x2 <- system.file("extdata/wgs/SEQC-II.wgs_coverage_metrics_tumor.csv.gz", package = "dracarys")
cm1 <- WgsCoverageMetricsFile$new(x1)
cm2 <- WgsCoverageMetricsFile$new(x2)
d1 <- read(cm1)
d2 <- read(cm2)
cm1$write(d1, out_dir = tempdir(), prefix = "seqc_n", out_format = "tsv")
cm2$write(d2, out_dir = tempdir(), prefix = "seqc_t", out_format = "tsv")