DragenFqc Object

Parses and tidies the DRAGEN FASTQC metrics file (fastqc_metrics.csv). Splits into 8 per-section sub-tables. Setting flat_tidy_names = TRUE gives flat dragenfqc_<section> tables rather than the concatenated form.

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenFqc

Public fields

flat_tidy_names

(logical(1))
drop the parser token so the 8 sub-tables are named dragenfqc_<section> (see nemo::Tool).

Methods

Public methods

• DragenFqc$new()

• DragenFqc$parse_posbasecontent()

• DragenFqc$tidy_posbasecontent()

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 DragenFqc object.

Usage

DragenFqc$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_posbasecontent()

Parse headerless section,mate,metric,value fastqc_metrics.csv into a long tibble.

Usage

DragenFqc$parse_posbasecontent(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_posbasecontent()

Tidy fastqc_metrics.csv into 8 long per-section sub-tables.

Usage

DragenFqc$tidy_posbasecontent(x)

Arguments

x

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

Examples

cls <- DragenFqc; tool <- "dragenfqc"
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 = "dragenfqc_.*parquet", full.names = FALSE))
#> [1] "sampleA_dragenfqc_posbasecontent.parquet" 
#> [2] "sampleA_dragenfqc_posbasemeanqual.parquet"
#> [3] "sampleA_dragenfqc_posqual.parquet"        
#> [4] "sampleA_dragenfqc_readgc.parquet"         
#> [5] "sampleA_dragenfqc_readgcqual.parquet"     
#> [6] "sampleA_dragenfqc_readlen.parquet"        
#> [7] "sampleA_dragenfqc_readmeanqual.parquet"   
#> [8] "sampleA_dragenfqc_seqpos.parquet"