Purple Object

Purple file parsing and manipulation.

Super class

nemo::Tool -> Purple

Methods

Public methods

• Purple$new()

• Purple$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 Purple object.

Usage

Purple$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 purple.qc file.

Usage

Purple$tidy_qc(x)

Arguments

x

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

Examples

cls <- Purple
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "purple_run1"
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = id)
(lf <- list.files(odir, pattern = "purple_.*parquet", full.names = FALSE))
#>  [1] "sample1_2_purple_cnvgenetsv.parquet"          
#>  [2] "sample1_2_purple_qc.parquet"                  
#>  [3] "sample1_germline_purple_drivercatalog.parquet"
#>  [4] "sample1_purple_cnvgenetsv.parquet"            
#>  [5] "sample1_purple_cnvsomtsv.parquet"             
#>  [6] "sample1_purple_germdeltsv.parquet"            
#>  [7] "sample1_purple_purityrange.parquet"           
#>  [8] "sample1_purple_puritytsv.parquet"             
#>  [9] "sample1_purple_qc.parquet"                    
#> [10] "sample1_purple_somclonality.parquet"          
#> [11] "sample1_purple_somhist.parquet"               
#> [12] "sample1_somatic_purple_drivercatalog.parquet" 
#> [13] "version_2_purple_version.parquet"             
#> [14] "version_purple_version.parquet"