DragenMap Object

Parses and tidies DRAGEN mapping/alignment outputs.

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenMap

Methods

Public methods

• DragenMap$new()

• DragenMap$tidy_metrics()

• DragenMap$tidy_umi()

• DragenMap$tidy_gc()

• DragenMap$tidy_time()

• DragenMap$parse_fraglenhist()

• DragenMap$parse_replay()

• DragenMap$tidy_replay()

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 DragenMap object.

Usage

DragenMap$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_metrics()

Tidy mapping_metrics.csv.

Usage

DragenMap$tidy_metrics(x)

Arguments

x

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

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Method tidy_umi()

Tidy umi_metrics.csv.

Usage

DragenMap$tidy_umi(x)

Arguments

x

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

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Method tidy_gc()

Tidy gc_metrics.csv.

Usage

DragenMap$tidy_gc(x)

Arguments

x

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

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Method tidy_time()

Tidy time_metrics.csv.

Usage

DragenMap$tidy_time(x)

Arguments

x

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

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Method parse_fraglenhist()

Parse fragment_length_hist.csv.

Usage

DragenMap$parse_fraglenhist(x)

Arguments

x

(character(1))
Path to file.

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Method parse_replay()

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

Usage

DragenMap$parse_replay(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_replay()

Tidy replay.json.

Usage

DragenMap$tidy_replay(x)

Arguments

x

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

Examples

cls <- DragenMap; tool <- "dragenmap"
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 = "dragenmap_.*parquet", full.names = FALSE))
#>  [1] "sampleA_dragenmap_fraglenhist.parquet"   
#>  [2] "sampleA_dragenmap_gcbias.parquet"        
#>  [3] "sampleA_dragenmap_gcmain.parquet"        
#>  [4] "sampleA_dragenmap_metrics.parquet"       
#>  [5] "sampleA_dragenmap_replayconfig.parquet"  
#>  [6] "sampleA_dragenmap_replaymain.parquet"    
#>  [7] "sampleA_dragenmap_time.parquet"          
#>  [8] "sampleA_dragenmap_trimmer.parquet"       
#>  [9] "sampleA_dragenmap_umihist.parquet"       
#> [10] "sampleA_dragenmap_umimain.parquet"       
#> [11] "sampleB_2_dragenmap_replayconfig.parquet"
#> [12] "sampleB_2_dragenmap_replaymain.parquet"  
#> [13] "sampleB_2_dragenmap_time.parquet"        
#> [14] "sampleB_dragenmap_replayconfig.parquet"  
#> [15] "sampleB_dragenmap_replaymain.parquet"    
#> [16] "sampleB_dragenmap_time.parquet"