Isofox Object

Isofox file parsing and manipulation.

Super class

nemo::Tool -> Isofox

Methods

Public methods

• Isofox$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 Isofox object.

Usage

Isofox$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 <- Isofox; tool <- "isofox"
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_isofox_altsj.parquet"         
#>  [2] "sample1_2_isofox_fusionsall.parquet"    
#>  [3] "sample1_2_isofox_fusionspass.parquet"   
#>  [4] "sample1_2_isofox_genecollection.parquet"
#>  [5] "sample1_2_isofox_genedata.parquet"      
#>  [6] "sample1_2_isofox_summary.parquet"       
#>  [7] "sample1_2_isofox_transdata.parquet"     
#>  [8] "sample1_isofox_altsj.parquet"           
#>  [9] "sample1_isofox_altsjunfilt.parquet"     
#> [10] "sample1_isofox_fusionsall.parquet"      
#> [11] "sample1_isofox_fusionspass.parquet"     
#> [12] "sample1_isofox_genecollection.parquet"  
#> [13] "sample1_isofox_genedata.parquet"        
#> [14] "sample1_isofox_retintron.parquet"       
#> [15] "sample1_isofox_summary.parquet"         
#> [16] "sample1_isofox_transdata.parquet"