DragenRna Object

Parses and tidies DRAGEN RNA outputs (gene-fusion statistics, quantification statistics).

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenRna

Methods

Public methods

• DragenRna$new()

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 DragenRna object.

Usage

DragenRna$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().

Examples

cls <- DragenRna; tool <- "dragenrna"
indir <- system.file("extdata", tool, package = "tidydragen")
odir <- tempdir()
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = "run1", output_id = "out1")
(lf <- list.files(odir, pattern = "dragenrna_.*parquet", full.names = FALSE))
#> [1] "sampleA_dragenrna_fusion.parquet" "sampleA_dragenrna_quant.parquet"