PloidyEstimationMetricsFile R6 Class

Contains methods for reading contents of the ploidy_estimation_metrics.csv file output from DRAGEN.

Super class

dracarys::File -> PloidyEstimationMetricsFile

Methods

Public methods

• PloidyEstimationMetricsFile$read()

• PloidyEstimationMetricsFile$write()

• PloidyEstimationMetricsFile$clone()

Inherited methods

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

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Method read()

Reads the ploidy_estimation_metrics.csv file output from DRAGEN.

Usage

PloidyEstimationMetricsFile$read()

Returns

tibble with one row and metrics spread across individual columns.

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Method write()

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

Usage

PloidyEstimationMetricsFile$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

PloidyEstimationMetricsFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

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