DragenTso Object

Parses and tidies the TSO500 ctDNA (cttsov2) app-layer outputs that sit alongside the DRAGEN metrics files: the CombinedVariantOutput small variants, DNA fusions, TMB trace / MSAF, and per-exon / per-gene coverage reports.

These files appear in both Results/<sample>/ and a Logs_Intermediates/ subdirectory (byte-identical). nemo matches on bname only, so the two copies would collide; refine_files() keeps the Results/ copy.

Super classes

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

Public fields

flat_tidy_names

(logical(1))
TRUE: outputs are named <tool>_<table> directly.

Methods

Public methods

• DragenTso$new()

• DragenTso$parse_smallvariants()

• DragenTso$parse_fusions()

• DragenTso$parse_sarinfo()

• DragenTso$tidy_sarinfo()

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 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().

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Method parse_smallvariants()

Parse only the [Small Variants] section of a CombinedVariantOutput.tsv file, dropping the rest (sourced from the SAR JSON instead).

Usage

DragenTso$parse_smallvariants(x)

Arguments

x

(character(1))
Path to file.

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Method parse_fusions()

Parse a Fusions.csv file (comment-prefixed header block, then a CSV table; may hold zero data rows).

Usage

DragenTso$parse_fusions(x)

Arguments

x

(character(1))
Path to file.

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Method parse_sarinfo()

Parse a SampleAnalysisResults.json file; returns its data block wrapped in a one-row tibble list-column. tidy_sarinfo() fans it out.

Usage

DragenTso$parse_sarinfo(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_sarinfo()

Fan a SampleAnalysisResults.json data block into six tables: sarinfo (sample info), sarqc (QC + expanded metrics + TMB/MSI biomarkers, wide), sarswds (Nirvana data sources), sarsw (software + Nirvana config), sarsnv (per-transcript small variants), sarcnv (CNVs).

Usage

DragenTso$tidy_sarinfo(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_sarinfo.parquet"      
#>  [6] "sampleA_dragentso_sarqc.parquet"        
#>  [7] "sampleA_dragentso_sarsnv.parquet"       
#>  [8] "sampleA_dragentso_sarsw.parquet"        
#>  [9] "sampleA_dragentso_sarswds.parquet"      
#> [10] "sampleA_dragentso_smallvariants.parquet"
#> [11] "sampleA_dragentso_tmbmsaf.parquet"      
#> [12] "sampleA_dragentso_tmbtrace.parquet"