Isofox Object

Isofox file parsing and manipulation.

Super class

nemo::Tool -> Isofox

Methods

Public methods

• Isofox$new()

• Isofox$parse_summary()

• Isofox$tidy_summary()

• Isofox$parse_genedata()

• Isofox$tidy_genedata()

• Isofox$parse_transdata()

• Isofox$tidy_transdata()

• Isofox$parse_altsj()

• Isofox$tidy_altsj()

• Isofox$parse_retintron()

• Isofox$tidy_retintron()

• Isofox$parse_fusionsall()

• Isofox$tidy_fusionsall()

• Isofox$parse_fusionspass()

• Isofox$tidy_fusionspass()

• Isofox$parse_genecollection()

• Isofox$tidy_genecollection()

• Isofox$clone()

Inherited methods

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

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Method new()

Create a new Isofox object.

Usage

Isofox$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 parse_summary()

Read summary.csv file.

Usage

Isofox$parse_summary(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_summary()

Tidy summary.csv file.

Usage

Isofox$tidy_summary(x)

Arguments

x

(character(1))
Path to file.

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Method parse_genedata()

Read gene_data.csv file.

Usage

Isofox$parse_genedata(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_genedata()

Tidy gene_data.csv file.

Usage

Isofox$tidy_genedata(x)

Arguments

x

(character(1))
Path to file.

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Method parse_transdata()

Read transcript_data.csv file.

Usage

Isofox$parse_transdata(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_transdata()

Tidy transcript_data.csv file.

Usage

Isofox$tidy_transdata(x)

Arguments

x

(character(1))
Path to file.

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Method parse_altsj()

Read alt_splice_junc.csv file.

Usage

Isofox$parse_altsj(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_altsj()

Tidy alt_splice_junc.csv file.

Usage

Isofox$tidy_altsj(x)

Arguments

x

(character(1))
Path to file.

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Method parse_retintron()

Read retained_intron.csv file.

Usage

Isofox$parse_retintron(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_retintron()

Tidy retained_intron.csv file.

Usage

Isofox$tidy_retintron(x)

Arguments

x

(character(1))
Path to file.

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Method parse_fusionsall()

Read fusions.csv file.

Usage

Isofox$parse_fusionsall(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_fusionsall()

Tidy fusions.csv file.

Usage

Isofox$tidy_fusionsall(x)

Arguments

x

(character(1))
Path to file.

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Method parse_fusionspass()

Read pass_fusions.csv file.

Usage

Isofox$parse_fusionspass(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_fusionspass()

Tidy pass_fusions.csv file.

Usage

Isofox$tidy_fusionspass(x)

Arguments

x

(character(1))
Path to file.

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Method parse_genecollection()

Read gene_collection.csv file.

Usage

Isofox$parse_genecollection(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_genecollection()

Tidy gene_collection.csv file.

Usage

Isofox$tidy_genecollection(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

Isofox$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

cls <- Isofox
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "isofox_run1"
obj <- cls$new(indir)
obj$nemofy(odir = odir, format = "parquet", id = id)
#> NULL
(lf <- list.files(odir, pattern = "parquet", full.names = FALSE))
#> character(0)
#TODO: add isofox test data