Amber Object

Amber file parsing and manipulation.

Super class

tidywigits::Tool -> Amber

Methods

Public methods

• Amber$new()

• Amber$parse_bafpcf()

• Amber$tidy_bafpcf()

• Amber$parse_baftsv()

• Amber$tidy_baftsv()

• Amber$parse_contaminationtsv()

• Amber$tidy_contaminationtsv()

• Amber$parse_homozygousregion()

• Amber$tidy_homozygousregion()

• Amber$parse_qc()

• Amber$tidy_qc()

• Amber$clone()

Inherited methods

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

---

Method new()

Create a new Amber object.

Usage

Amber$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.

---

Method parse_bafpcf()

Read baf.pcf file.

Usage

Amber$parse_bafpcf(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_bafpcf()

Tidy baf.pcf file.

Usage

Amber$tidy_bafpcf(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_baftsv()

Read baf.tsv.gz file.

Usage

Amber$parse_baftsv(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_baftsv()

Tidy baf.tsv.gz file.

Usage

Amber$tidy_baftsv(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_contaminationtsv()

Read contamination.tsv file.

Usage

Amber$parse_contaminationtsv(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_contaminationtsv()

Tidy contamination.tsv file.

Usage

Amber$tidy_contaminationtsv(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_homozygousregion()

Read homozygousregion.tsv file.

Usage

Amber$parse_homozygousregion(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_homozygousregion()

Tidy homozygousregion.tsv file.

Usage

Amber$tidy_homozygousregion(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_qc()

Read qc file.

Usage

Amber$parse_qc(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_qc()

Tidy qc file.

Usage

Amber$tidy_qc(x)

Arguments

x

(character(1))
Path to file.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Amber$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
path <- here::here(
  "nogit/oa_v1"
)
a <- Amber$new(path)
} # }