Sage Object

Sage file parsing and manipulation.

Super class

tidywigits::Tool -> Sage

Methods

Public methods

• Sage$new()

• Sage$parse_bqrtsv()

• Sage$tidy_bqrtsv()

• Sage$parse_genecvg()

• Sage$tidy_genecvg()

• Sage$parse_exoncvg()

• Sage$tidy_exoncvg()

• Sage$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()

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Method new()

Create a new Sage object.

Usage

Sage$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 parse_bqrtsv()

Read bqr.tsv file.

Usage

Sage$parse_bqrtsv(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_bqrtsv()

Tidy bqr.tsv file.

Usage

Sage$tidy_bqrtsv(x)

Arguments

x

(character(1))
Path to file.

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Method parse_genecvg()

Read gene.coverage.tsv file.

Usage

Sage$parse_genecvg(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_genecvg()

Tidy gene.coverage.tsv file.

Usage

Sage$tidy_genecvg(x)

Arguments

x

(character(1))
Path to file.

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Method parse_exoncvg()

Read exon.medians.tsv file.

Usage

Sage$parse_exoncvg(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_exoncvg()

Tidy exon.medians.tsv file.

Usage

Sage$tidy_exoncvg(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

Sage$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

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