DragenCov Object

Parses and tidies DRAGEN coverage outputs (per-contig mean coverage, coverage metrics, fine histograms, and coverage-report BEDs). Some files fan out into multiple output tables: tidy_metricsmain splits the coverage metrics into metricsmain/metricsbins/metricscumu, and tidy_reportbedmain splits the coverage-report BED into reportbedmain/reportbedcumu. Every other table has tidy_name == parser, so its name is unchanged. The per-method docs below cover each table's specifics.

The coverage region (wgs / tmb /qc-coverage-region-{<region>}) and phenotype (normal / tumor) are folded from the filename into the output prefix by DragenTool's refine_files() hook, so one schema table serves every region/phenotype variant.

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenCov

Public fields

flat_tidy_names

(logical(1))
TRUE: fanned-out sub-tables are named <tool>_<tidy_name> directly (parser token dropped), so each sub-table's name is its final output table. See the class description for the fan-out map.

Methods

Public methods

• DragenCov$new()

• DragenCov$tidy_metricsmain()

• DragenCov$parse_finehist()

• DragenCov$parse_reportbedmain()

• DragenCov$tidy_reportbedmain()

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 DragenCov object.

Usage

DragenCov$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 tidy_metricsmain()

Tidy *_coverage_metrics.csv into metricsmain (wide summary), metricsbins (bucketed depth histogram), and metricscumu (cumulative).

Usage

DragenCov$tidy_metricsmain(x)

Arguments

x

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

---

Method parse_finehist()

Parse *_fine_hist.csv, returning depth as an integer.

Usage

DragenCov$parse_finehist(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_reportbedmain()

Parse *_cov_report.bed; tidy_reportbedmain() types and splits it.

Usage

DragenCov$parse_reportbedmain(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_reportbedmain()

Tidy *_cov_report.bed into reportbedmain (per-interval distribution stats, wide) and reportbedcumu (coverage thresholds, long).

Usage

DragenCov$tidy_reportbedmain(x)

Arguments

x

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

Examples

cls <- DragenCov; tool <- "dragencov"
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 = "dragencov_.*parquet", full.names = FALSE))
#>  [1] "sampleA_exon_dragencov_metricsbins.parquet"      
#>  [2] "sampleA_exon_dragencov_metricscumu.parquet"      
#>  [3] "sampleA_exon_dragencov_metricsmain.parquet"      
#>  [4] "sampleA_target_bed_dragencov_metricsbins.parquet"
#>  [5] "sampleA_target_bed_dragencov_metricscumu.parquet"
#>  [6] "sampleA_target_bed_dragencov_metricsmain.parquet"
#>  [7] "sampleA_umccr_dragencov_readreportbed.parquet"   
#>  [8] "sampleA_umccr_dragencov_reportbedcumu.parquet"   
#>  [9] "sampleA_umccr_dragencov_reportbedmain.parquet"   
#> [10] "sampleA_wgs_dragencov_contigmean.parquet"        
#> [11] "sampleA_wgs_dragencov_finehist.parquet"          
#> [12] "sampleA_wgs_dragencov_metricsbins.parquet"       
#> [13] "sampleA_wgs_dragencov_metricscumu.parquet"       
#> [14] "sampleA_wgs_dragencov_metricsmain.parquet"       
#> [15] "sampleA_wgs_normal_dragencov_contigmean.parquet" 
#> [16] "sampleA_wgs_tumor_dragencov_contigmean.parquet"