TsoAlignCollapseFusionCallerMetricsFile R6 Class

Contains methods for reading and displaying contents of the AlignCollapseFusionCaller_metrics.json.gz file output from TSO.

Super class

dracarys::File -> TsoAlignCollapseFusionCallerMetricsFile

Methods

Public methods

• TsoAlignCollapseFusionCallerMetricsFile$read()

• TsoAlignCollapseFusionCallerMetricsFile$write()

• TsoAlignCollapseFusionCallerMetricsFile$plot()

• TsoAlignCollapseFusionCallerMetricsFile$clone()

Inherited methods

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

---

Method read()

Reads the AlignCollapseFusionCaller_metrics.json.gz file output from TSO.

Usage

TsoAlignCollapseFusionCallerMetricsFile$read()

Returns

tibble with the following columns:

• section: name of original JSON element

• name: name of metric

• value: value of metric

• percent: percentage

---

Method write()

Writes a tidy version of the AlignCollapseFusionCaller_metrics.json.gz file output from TSO.

Histo is the majority from UmiStatistics section, write out separately. Histo of num supporting fragments: Num of families with 0/1/2/3... raw reads. Histo of unique UMIs per fragment pos: Num of pos with 0/1/2/3... UMI seqs.

Usage

TsoAlignCollapseFusionCallerMetricsFile$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) (one of 'tsv' (def.), 'parquet', 'both').

drid

dracarys ID to use for the dataset (e.g. wfrid.123, prid.456).

---

Method plot()

Generates the UmiStatistics Histogram plots from the AlignCollapseFusionCaller_metrics.json.gz file output from TSO.

• Histo is the majority from UmiStatistics section, deal with it separately.

• Histo of num supporting fragments: Num of families with 0/1/2/3... raw reads.

• Histo of unique UMIs per fragment pos: Num of pos with 0/1/2/3... UMI seqs.

Usage

TsoAlignCollapseFusionCallerMetricsFile$plot(d, max_num = 15)

Arguments

d

Parsed object from self$read().

max_num

Maximum number to display in both plots.

Returns

Both histogram plot objects.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TsoAlignCollapseFusionCallerMetricsFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

x <- system.file("extdata/tso/sample705.AlignCollapseFusionCaller_metrics.json.gz",
  package = "dracarys"
)
m <- TsoAlignCollapseFusionCallerMetricsFile$new(x)
d_parsed <- m$read() # or read(m)
m$write(d_parsed, out_dir = tempdir(), prefix = "sample705", out_format = c("tsv", "rds"))