DragenVar Object

Parses and tidies DRAGEN variant-related metric outputs (variant caller, SV, CNV, ploidy, TMB, HRD, etc.).

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenVar

Public fields

flat_tidy_names

(logical(1))
TRUE: fan-out sub-tables are named <tool>_<tidy_name> (parser token dropped). Needed for the ploidystats/ploidyratio split.

Methods

Public methods

• DragenVar$new()

• DragenVar$tidy_vc()

• DragenVar$tidy_gvcf()

• DragenVar$tidy_cnv()

• DragenVar$tidy_hethom()

• DragenVar$tidy_ploidystats()

• DragenVar$tidy_nuctrans()

• DragenVar$parse_microsat()

• DragenVar$parse_contamination()

• DragenVar$parse_ploidyvcf()

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 DragenVar object.

Usage

DragenVar$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 tidy_vc()

Tidy vc_metrics.csv. rg (sample id) kept raw; region moved from metric names into a region column.

Usage

DragenVar$tidy_vc(x)

Arguments

x

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

---

Method tidy_gvcf()

Tidy gvcf_metrics.csv (gVCF postfilter). Same shape as vc_metrics; region moved into a region column.

Usage

DragenVar$tidy_gvcf(x)

Arguments

x

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

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Method tidy_cnv()

Tidy cnv_metrics.csv.

Usage

DragenVar$tidy_cnv(x)

Arguments

x

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

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Method tidy_hethom()

Tidy vc_hethom_ratio_metrics.csv.

Usage

DragenVar$tidy_hethom(x)

Arguments

x

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

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Method tidy_ploidystats()

Tidy ploidy_estimation_metrics.csv into ploidystats (sample scalars) and ploidyratio (long, one row per chromosome ratio).

Usage

DragenVar$tidy_ploidystats(x)

Arguments

x

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

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Method tidy_nuctrans()

Tidy allele_transition_noise_metrics.csv

Usage

DragenVar$tidy_nuctrans(x)

Arguments

x

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

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Method parse_microsat()

Parse microsat_output.json (MSI).

Usage

DragenVar$parse_microsat(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_contamination()

Parse contamination.json (cttso cross-sample contamination). Flat JSON; the per-SNP SNPsUsed array is dropped, NaN p-value -> NA.

Usage

DragenVar$parse_contamination(x)

Arguments

x

(character(1))
Path to file.

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Method parse_ploidyvcf()

Parse ploidy.vcf.gz depth-of-coverage dc and normalised depth ndc.

Usage

DragenVar$parse_ploidyvcf(x)

Arguments

x

(character(1))
Path to file.

Examples

cls <- DragenVar; tool <- "dragenvar"
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 = "dragenvar_.*parquet", full.names = FALSE))
#>  [1] "sampleA_dragenvar_cnv.parquet"          
#>  [2] "sampleA_dragenvar_contamination.parquet"
#>  [3] "sampleA_dragenvar_gvcf.parquet"         
#>  [4] "sampleA_dragenvar_hethom.parquet"       
#>  [5] "sampleA_dragenvar_hrd.parquet"          
#>  [6] "sampleA_dragenvar_microsat.parquet"     
#>  [7] "sampleA_dragenvar_nuctrans.parquet"     
#>  [8] "sampleA_dragenvar_ploidyratio.parquet"  
#>  [9] "sampleA_dragenvar_ploidystats.parquet"  
#> [10] "sampleA_dragenvar_ploidyvcf.parquet"    
#> [11] "sampleA_dragenvar_sv.parquet"           
#> [12] "sampleA_dragenvar_tmb.parquet"          
#> [13] "sampleA_dragenvar_vc.parquet"           
#> [14] "sampleB_dragenvar_cnv.parquet"          
#> [15] "sampleB_dragenvar_ploidyratio.parquet"  
#> [16] "sampleB_dragenvar_ploidystats.parquet"  
#> [17] "sampleB_dragenvar_vc.parquet"