Purple Object

Purple file parsing and manipulation.

Super class

tidywigits::Tool -> Purple

Methods

Public methods

• Purple$new()

• Purple$list_files()

• Purple$parse_qc()

• Purple$tidy_qc()

• Purple$parse_cnvgenetsv()

• Purple$tidy_cnvgenetsv()

• Purple$parse_cnvsomtsv()

• Purple$tidy_cnvsomtsv()

• Purple$parse_drivercatalog()

• Purple$tidy_drivercatalog()

• Purple$parse_germdeltsv()

• Purple$tidy_germdeltsv()

• Purple$parse_purityrange()

• Purple$tidy_purityrange()

• Purple$parse_puritytsv()

• Purple$tidy_puritytsv()

• Purple$parse_somclonality()

• Purple$tidy_somclonality()

• Purple$parse_somhist()

• Purple$tidy_somhist()

• Purple$parse_version()

• Purple$tidy_version()

• Purple$clone()

Inherited methods

• tidywigits::Tool$.eval_func()
• tidywigits::Tool$.parse_file()
• tidywigits::Tool$.parse_file_nohead()
• tidywigits::Tool$.tidy_file()
• tidywigits::Tool$filter_files()
• tidywigits::Tool$nemofy()
• tidywigits::Tool$print()
• tidywigits::Tool$tidy()
• tidywigits::Tool$write()

---

Method new()

Create a new Purple object.

Usage

Purple$new(path = NULL, files_tbl = NULL)

Arguments

path

(character(1))
Output directory of tool. If files_tbl is supplied, this basically gets ignored.

files_tbl

(tibble(n))
Tibble of files from list_files_dir.

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Method list_files()

List files in given purple directory. Overwrites parent class to handle germline driver.catalog files.

Usage

Purple$list_files(type = "file")

Arguments

type

(character(1))
File type(s) to return (e.g. any, file, directory, symlink). See fs::dir_info.

Returns

A tibble of file paths.

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Method parse_qc()

Read purple.qc file.

Usage

Purple$parse_qc(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_qc()

Tidy purple.qc file.

Usage

Purple$tidy_qc(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_cnvgenetsv()

Read purple.cnv.gene.tsv file.

Usage

Purple$parse_cnvgenetsv(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_cnvgenetsv()

Tidy purple.cnv.gene.tsv file.

Usage

Purple$tidy_cnvgenetsv(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_cnvsomtsv()

Read purple.cnv.somatic.tsv file.

Usage

Purple$parse_cnvsomtsv(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_cnvsomtsv()

Tidy purple.cnv.somatic.tsv file.

Usage

Purple$tidy_cnvsomtsv(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_drivercatalog()

Read purple.driver.catalog.germline|somatic.tsv file.

Usage

Purple$parse_drivercatalog(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_drivercatalog()

Tidy purple.driver.catalog.germline|somatic.tsv file.

Usage

Purple$tidy_drivercatalog(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_germdeltsv()

Read purple.germline.deletion.tsv file.

Usage

Purple$parse_germdeltsv(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_germdeltsv()

Tidy purple.germline.deletion.tsv file.

Usage

Purple$tidy_germdeltsv(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_purityrange()

Read purple.purity.range.tsv file.

Usage

Purple$parse_purityrange(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_purityrange()

Tidy purple.purity.range.tsv file.

Usage

Purple$tidy_purityrange(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_puritytsv()

Read purple.purity.tsv file.

Usage

Purple$parse_puritytsv(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_puritytsv()

Tidy purple.purity.tsv file.

Usage

Purple$tidy_puritytsv(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_somclonality()

Read purple.somatic.clonality.tsv file.

Usage

Purple$parse_somclonality(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_somclonality()

Tidy purple.somatic.clonality.tsv file.

Usage

Purple$tidy_somclonality(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_somhist()

Read purple.somatic.hist.tsv file.

Usage

Purple$parse_somhist(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_somhist()

Tidy purple.somatic.hist.tsv file.

Usage

Purple$tidy_somhist(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_version()

Read purple.version file.

Usage

Purple$parse_version(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_version()

Tidy purple.version file.

Usage

Purple$tidy_version(x)

Arguments

x

(character(1))
Path to file.

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Method clone()

The objects of this class are cloneable with this method.

Usage

Purple$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
path <- here::here(
  "nogit"
)
p <- Purple$new(path)
p$tidy()
p$tbls$tidy |>
  purrr::set_names(p$tbls$parser) |>
  purrr::map(\(x) x[["data"]][[1]])
} # }