DragenTso Object

Parses and tidies TSO500 ctDNA (cttsov2) app-layer outputs.

These files are duplicated under Results/ and Logs_Intermediates/; refine_files() keeps the Results/ copy.

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenTso

Methods

Public methods

• DragenTso$new()

• DragenTso$parse_smallvariants()

• DragenTso$parse_fusions()

• DragenTso$parse_sar()

• DragenTso$tidy_sar()

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()

---

Method new()

Create a new DragenTso object.

Usage

DragenTso$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().

---

Method parse_smallvariants()

Parse the [Small Variants] section of CombinedVariantOutput.tsv (the rest comes from the SAR JSON).

Usage

DragenTso$parse_smallvariants(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_fusions()

Parse Fusions.csv.

Usage

DragenTso$parse_fusions(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_sar()

Parse SampleAnalysisResults.json into a one-row list-column tibble.

Usage

DragenTso$parse_sar(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_sar()

Tidy SampleAnalysisResults.json.

Usage

DragenTso$tidy_sar(x)

Arguments

x

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

Examples

cls <- DragenTso; tool <- "dragentso"
indir <- system.file("extdata", tool, package = "tidydragen")
odir <- tempdir()
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = "run1")
(lf <- list.files(odir, pattern = "dragentso_.*parquet", full.names = FALSE))
#>  [1] "sampleA_dragentso_exoncov.parquet"      
#>  [2] "sampleA_dragentso_fusions.parquet"      
#>  [3] "sampleA_dragentso_genecov.parquet"      
#>  [4] "sampleA_dragentso_sarcnv.parquet"       
#>  [5] "sampleA_dragentso_sarmain.parquet"      
#>  [6] "sampleA_dragentso_sarqc.parquet"        
#>  [7] "sampleA_dragentso_sarqcthr.parquet"     
#>  [8] "sampleA_dragentso_sarsnv.parquet"       
#>  [9] "sampleA_dragentso_sarsw.parquet"        
#> [10] "sampleA_dragentso_sarswds.parquet"      
#> [11] "sampleA_dragentso_smallvariants.parquet"
#> [12] "sampleA_dragentso_tmbmsaf.parquet"      
#> [13] "sampleA_dragentso_tmbtrace.parquet"