TsoFusionsCsvFile R6 Class

Contains methods for reading and displaying contents of the Fusions.csv file output from TSO. Returns a tibble where the columns are (based on the input file header metadata):

• Sample: input sample ID.

• Name: Fusion name as reported by manta.

• Chr1/Chr2: The chromosome of the 1st/2nd breakend.

• Pos1/Pos2: The position of the 1st/2nd breakend.

• Direction: The direction of how the breakends are joined together.

• Alt_Depth: The number of read-pairs supporting the fusion call.

• BP1_Depth/BP2_Depth: Number of read-pairs aligned to the 1st/2nd breakend.

• Total_Depth: Max number of read-pairs aligned to a fusion breakend.

• VAF: Variant allele frequency.

• Gene1/Gene2: Genes that overlap the 1st/2nd breakend.

• Contig: The fusion contig.

• Filter: Indicates whether the fusion has passed all of the fusion filters.

• Is_Cosmic_GenePair: Indicates whether the gene pair has been reported by Cosmic(True/False).

Super class

dracarys::File -> TsoFusionsCsvFile

Methods

Public methods

• TsoFusionsCsvFile$read()

• TsoFusionsCsvFile$write()

• TsoFusionsCsvFile$clone()

Inherited methods

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

---

Method read()

Reads the Fusions.csv file output from TSO.

Usage

TsoFusionsCsvFile$read()

Returns

tibble with several columns.

---

Method write()

Writes a tidy version of the Fusions.csv file output from TSO.

Usage

TsoFusionsCsvFile$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

TsoFusionsCsvFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

x <- system.file("extdata/tso/sample705_Fusions.csv", package = "dracarys")
fus <- TsoFusionsCsvFile$new(x)
d_parsed <- fus$read() # or read(fus)
fus$write(d_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv")