DragenCov Object

Parses and tidies DRAGEN coverage outputs.

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

Methods

Public methods

• DragenCov$new()

• DragenCov$tidy_covmetrics()

• DragenCov$parse_finehist()

• DragenCov$parse_reportbed()

• DragenCov$tidy_reportbed()

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 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().

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Method tidy_covmetrics()

Tidy *_coverage_metrics.csv.

Usage

DragenCov$tidy_covmetrics(x)

Arguments

x

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

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Method parse_finehist()

Parse *_fine_hist.csv.

Usage

DragenCov$parse_finehist(x)

Arguments

x

(character(1))
Path to file.

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Method parse_reportbed()

Parse *_cov_report.bed.

Usage

DragenCov$parse_reportbed(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_reportbed()

Tidy *_cov_report.bed.

Usage

DragenCov$tidy_reportbed(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"