Amber Object

Amber file parsing and manipulation.

Super class

nemo::Tool -> Amber

Methods

Public methods

• Amber$new()

• Amber$tidy_qc()

Inherited methods

• nemo::Tool$filter_files()
• nemo::Tool$get_metadata()
• nemo::Tool$get_tbls()
• nemo::Tool$list_files()
• nemo::Tool$print()
• nemo::Tool$run()
• nemo::Tool$tidy()
• nemo::Tool$write()

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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 is ignored.

files_tbl

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

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Method tidy_qc()

Tidy qc file.

Usage

Amber$tidy_qc(x)

Arguments

x

(character(1) or tibble())
Path to file or already parsed tibble.

Examples

cls <- Amber
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "amber_run1"
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = id)
(lf <- list.files(odir, pattern = "amber_.*parquet", full.names = FALSE))
#> [1] "sample1_amber_bafpcf.parquet"          
#> [2] "sample1_amber_contaminationtsv.parquet"
#> [3] "sample1_amber_homozygousregion.parquet"
#> [4] "sample1_amber_qc.parquet"