FastqcMetrics R6 Class

Contains methods for reading and displaying contents of the fastqc_metrics.csv file output from DRAGEN.

Super class

dracarys::File -> FastqcMetricsFile

Methods

Public methods

• FastqcMetricsFile$read()

• FastqcMetricsFile$write()

• FastqcMetricsFile$clone()

Inherited methods

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

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Method read()

Reads the fastqc_metrics.csv file output from DRAGEN.

Usage

FastqcMetricsFile$read()

Returns

tibble. TODO.

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Method write()

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

Usage

FastqcMetricsFile$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

FastqcMetricsFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

x <- system.file("extdata/wgs/SEQC-II.fastqc_metrics.csv.gz", package = "dracarys")
fq <- FastqcMetricsFile$new(x)
d <- fq$read()
fq$write(d, out_dir = tempdir(), prefix = "seqc_fq", out_format = "tsv")
# fq$plot(d)