Linx Object

Linx file parsing and manipulation.

Super class

nemo::Tool -> Linx

Methods

Public methods

• Linx$new()

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()

---

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 is ignored.

files_tbl

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

Examples

cls <- Linx
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "linx_run1"
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = id)
(lf <- list.files(odir, pattern = "linx_.*parquet", full.names = FALSE))
#>  [1] "sample1_2_linx_viscn.parquet"               
#>  [2] "sample1_2_linx_visfusion.parquet"           
#>  [3] "sample1_2_linx_visgeneexon.parquet"         
#>  [4] "sample1_2_linx_visproteindomain.parquet"    
#>  [5] "sample1_2_linx_vissegments.parquet"         
#>  [6] "sample1_2_linx_vissvdata.parquet"           
#>  [7] "sample1_germline_2_linx_breakends.parquet"  
#>  [8] "sample1_germline_linx_breakends.parquet"    
#>  [9] "sample1_germline_linx_clusters.parquet"     
#> [10] "sample1_germline_linx_drivercatalog.parquet"
#> [11] "sample1_germline_linx_links.parquet"        
#> [12] "sample1_germline_linx_svs.parquet"          
#> [13] "sample1_linx_drivers.parquet"               
#> [14] "sample1_linx_fusions.parquet"               
#> [15] "sample1_linx_viscn.parquet"                 
#> [16] "sample1_linx_visfusion.parquet"             
#> [17] "sample1_linx_visgeneexon.parquet"           
#> [18] "sample1_linx_visproteindomain.parquet"      
#> [19] "sample1_linx_vissegments.parquet"           
#> [20] "sample1_linx_vissvdata.parquet"             
#> [21] "sample1_somatic_2_linx_breakends.parquet"   
#> [22] "sample1_somatic_linx_breakends.parquet"     
#> [23] "sample1_somatic_linx_clusters.parquet"      
#> [24] "sample1_somatic_linx_drivercatalog.parquet" 
#> [25] "sample1_somatic_linx_links.parquet"         
#> [26] "sample1_somatic_linx_svs.parquet"           
#> [27] "version_2_linx_version.parquet"             
#> [28] "version_3_linx_version.parquet"             
#> [29] "version_4_linx_version.parquet"             
#> [30] "version_linx_version.parquet"