Purple Object

Purple file parsing and manipulation.

Super class

nemo::Tool -> Purple

Methods

Public methods

• Purple$new()

Inherited methods

• nemo::Tool$filter_files()
• nemo::Tool$get_globs()
• 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().

Examples

cls <- Purple; tool <- "purple"
indir <- system.file("extdata/oa", tool, package = "tidywigits")
odir <- tempdir()
id <- paste0(tool, "_run1")
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = id)
(lf <- list.files(odir, pattern = paste0(tool, "_.*parquet"), full.names = FALSE))
#>  [1] "sample1_2_purple_cnvgenetsv.parquet"            
#>  [2] "sample1_2_purple_qc.parquet"                    
#>  [3] "sample1_3_purple_cnvgenetsv.parquet"            
#>  [4] "sample1_germline_2_purple_drivercatalog.parquet"
#>  [5] "sample1_germline_purple_drivercatalog.parquet"  
#>  [6] "sample1_purple_chromarm.parquet"                
#>  [7] "sample1_purple_cnvgenetsv.parquet"              
#>  [8] "sample1_purple_cnvsomtsv.parquet"               
#>  [9] "sample1_purple_germampdel.parquet"              
#> [10] "sample1_purple_germdeltsv.parquet"              
#> [11] "sample1_purple_purityrange.parquet"             
#> [12] "sample1_purple_puritytsv.parquet"               
#> [13] "sample1_purple_qc.parquet"                      
#> [14] "sample1_purple_somclonality.parquet"            
#> [15] "sample1_purple_somhist.parquet"                 
#> [16] "sample1_somatic_2_purple_drivercatalog.parquet" 
#> [17] "sample1_somatic_purple_drivercatalog.parquet"   
#> [18] "version_2_purple_version.parquet"               
#> [19] "version_purple_version.parquet"