Linx Object

Linx file parsing and manipulation.

Super class

nemo::Tool -> Linx

Methods

Public methods

• Linx$new()

• Linx$list_files()

• Linx$parse_breakends()

• Linx$tidy_breakends()

• Linx$parse_clusters()

• Linx$tidy_clusters()

• Linx$parse_drivercatalog()

• Linx$tidy_drivercatalog()

• Linx$parse_drivers()

• Linx$tidy_drivers()

• Linx$parse_fusions()

• Linx$tidy_fusions()

• Linx$parse_links()

• Linx$tidy_links()

• Linx$parse_neoepitope()

• Linx$tidy_neoepitope()

• Linx$parse_svs()

• Linx$tidy_svs()

• Linx$parse_viscn()

• Linx$tidy_viscn()

• Linx$parse_visfusion()

• Linx$tidy_visfusion()

• Linx$parse_visgeneexon()

• Linx$tidy_visgeneexon()

• Linx$parse_visproteindomain()

• Linx$tidy_visproteindomain()

• Linx$parse_vissegments()

• Linx$tidy_vissegments()

• Linx$parse_vissvdata()

• Linx$tidy_vissvdata()

• Linx$parse_version()

• Linx$tidy_version()

• Linx$clone()

Inherited methods

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

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Method new()

Create a new Linx object.

Usage

Linx$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 nemo::list_files_dir().

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Method list_files()

List files in given linx directory. Overwrites parent class to handle germline LINX files.

Usage

Linx$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_breakends()

Read breakend.tsv file.

Usage

Linx$parse_breakends(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_breakends()

Tidy breakend.tsv file.

Usage

Linx$tidy_breakends(x)

Arguments

x

(character(1))
Path to file.

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Method parse_clusters()

Read clusters.tsv file.

Usage

Linx$parse_clusters(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_clusters()

Tidy clusters.tsv file.

Usage

Linx$tidy_clusters(x)

Arguments

x

(character(1))
Path to file.

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Method parse_drivercatalog()

Read linx.driver.catalog.tsv file.

Usage

Linx$parse_drivercatalog(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_drivercatalog()

Tidy linx.driver.catalog.tsv file.

Usage

Linx$tidy_drivercatalog(x)

Arguments

x

(character(1))
Path to file.

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Method parse_drivers()

Read linx.drivers.tsv file.

Usage

Linx$parse_drivers(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_drivers()

Tidy linx.drivers.tsv file.

Usage

Linx$tidy_drivers(x)

Arguments

x

(character(1))
Path to file.

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Method parse_fusions()

Read linx.fusion.tsv file.

Usage

Linx$parse_fusions(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_fusions()

Tidy linx.fusion.tsv file.

Usage

Linx$tidy_fusions(x)

Arguments

x

(character(1))
Path to file.

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Method parse_links()

Read links.tsv file.

Usage

Linx$parse_links(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_links()

Tidy links.tsv file.

Usage

Linx$tidy_links(x)

Arguments

x

(character(1))
Path to file.

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Method parse_neoepitope()

Read neoepitope.tsv file.

Usage

Linx$parse_neoepitope(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_neoepitope()

Tidy neoepitope.tsv file.

Usage

Linx$tidy_neoepitope(x)

Arguments

x

(character(1))
Path to file.

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Method parse_svs()

Read svs.tsv file.

Usage

Linx$parse_svs(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_svs()

Tidy svs.tsv file.

Usage

Linx$tidy_svs(x)

Arguments

x

(character(1))
Path to file.

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Method parse_viscn()

Read linx.vis_copy_number.tsv file.

Usage

Linx$parse_viscn(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_viscn()

Tidy linx.vis_copy_number.tsv file.

Usage

Linx$tidy_viscn(x)

Arguments

x

(character(1))
Path to file.

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Method parse_visfusion()

Read linx.vis_fusion.tsv file.

Usage

Linx$parse_visfusion(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_visfusion()

Tidy linx.vis_fusion.tsv file.

Usage

Linx$tidy_visfusion(x)

Arguments

x

(character(1))
Path to file.

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Method parse_visgeneexon()

Read linx.vis_gene_exon.tsv file.

Usage

Linx$parse_visgeneexon(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_visgeneexon()

Tidy linx.vis_gene_exon.tsv file.

Usage

Linx$tidy_visgeneexon(x)

Arguments

x

(character(1))
Path to file.

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Method parse_visproteindomain()

Read linx.vis_protein_domain.tsv file.

Usage

Linx$parse_visproteindomain(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_visproteindomain()

Tidy linx.vis_protein_domain.tsv file.

Usage

Linx$tidy_visproteindomain(x)

Arguments

x

(character(1))
Path to file.

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Method parse_vissegments()

Read linx.vis_segments.tsv file.

Usage

Linx$parse_vissegments(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_vissegments()

Tidy linx.vis_segments.tsv file.

Usage

Linx$tidy_vissegments(x)

Arguments

x

(character(1))
Path to file.

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Method parse_vissvdata()

Read linx.vis_sv_data.tsv file.

Usage

Linx$parse_vissvdata(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_vissvdata()

Tidy linx.vis_sv_data.tsv file.

Usage

Linx$tidy_vissvdata(x)

Arguments

x

(character(1))
Path to file.

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Method parse_version()

Read linx.version file.

Usage

Linx$parse_version(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_version()

Tidy linx.version file.

Usage

Linx$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

Linx$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

cls <- Linx
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "linx_run1"
obj <- cls$new(indir)
obj$nemofy(odir = odir, format = "parquet", id = id)
#> NULL
(lf <- list.files(odir, pattern = "linx.*parquet", full.names = FALSE))
#> character(0)