Tool1 Object

Parses and tidies output files from Tool1. Table schemas and file patterns are defined in inst/config/tools/tool1/schema.yaml. Custom parse and tidy methods are provided for tables that require non-standard handling.

Super class

nemo::Tool -> Tool1

Methods

Public methods

• Tool1$new()

• Tool1$tidy_table3()

• Tool1$parse_table5()

• Tool1$tidy_table5()

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 Tool1 object.

Usage

Tool1$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 list_files_dir().

Returns

(R6::R6Class())
R6 object.

---

Method tidy_table3()

Tidy table3.tsv file with type conversion enabled.

Usage

Tool1$tidy_table3(x)

Arguments

x

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

Returns

(tibble())
Tidy data in enframed tibble.

---

Method parse_table5()

Read table5.csv file (csv, no header, long format).

Usage

Tool1$parse_table5(x)

Arguments

x

(character(1))
Path to file.

Returns

(tibble())
Raw parsed tibble with columns section, rg, variable, count, pct.

---

Method tidy_table5()

Tidy table5.csv file.

Usage

Tool1$tidy_table5(x)

Arguments

x

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

Returns

(tibble())
Tidy data in enframed tibble, pivoted wide from long format.

Examples

indir <- system.file("extdata/tool1", package = "nemo")
dir1 <- tempdir()
obj1 <- Tool1$new(indir)

p3 <- system.file("extdata/tool1/latest/sampleA.tool1.table3.tsv", package = "nemo")
p5 <- system.file("extdata/tool1/latest/sampleA.tool1.table5.csv", package = "nemo")
(tidy3 <- obj1$tidy_table3(p3))
#> # A tibble: 1 × 2
#>   name   data            
#>   <chr>  <list>          
#> 1 table3 <tibble [1 × 5]>
(raw5 <- obj1$parse_table5(p5))
#> # A tibble: 16 × 5
#>    section                         rg         variable           count    pct
#>    <chr>                           <chr>      <chr>              <dbl>  <dbl>
#>  1 TUMOR MAPPING/ALIGNING SUMMARY  NA         Total reads      3000000 100   
#>  2 TUMOR MAPPING/ALIGNING SUMMARY  NA         Mapped reads     2900000  96.7 
#>  3 TUMOR MAPPING/ALIGNING SUMMARY  NA         Unmapped reads    100000   3.33
#>  4 TUMOR MAPPING/ALIGNING SUMMARY  NA         Total bases    450000000  NA   
#>  5 NORMAL MAPPING/ALIGNING SUMMARY NA         Total reads      1500000 100   
#>  6 NORMAL MAPPING/ALIGNING SUMMARY NA         Mapped reads     1460000  97.3 
#>  7 NORMAL MAPPING/ALIGNING SUMMARY NA         Unmapped reads     40000   2.67
#>  8 NORMAL MAPPING/ALIGNING SUMMARY NA         Total bases    226500000  NA   
#>  9 TUMOR MAPPING/ALIGNING PER RG   BC01.1.FC1 Total reads      3000000 100   
#> 10 TUMOR MAPPING/ALIGNING PER RG   BC01.1.FC1 Mapped reads     2900000  96.7 
#> 11 TUMOR MAPPING/ALIGNING PER RG   BC01.1.FC1 Unmapped reads    100000   3.33
#> 12 TUMOR MAPPING/ALIGNING PER RG   BC01.1.FC1 Total bases    450000000  NA   
#> 13 NORMAL MAPPING/ALIGNING PER RG  BC02.1.FC1 Total reads      1500000 100   
#> 14 NORMAL MAPPING/ALIGNING PER RG  BC02.1.FC1 Mapped reads     1460000  97.3 
#> 15 NORMAL MAPPING/ALIGNING PER RG  BC02.1.FC1 Unmapped reads     40000   2.67
#> 16 NORMAL MAPPING/ALIGNING PER RG  BC02.1.FC1 Total bases    226500000  NA   
(tidy5 <- obj1$tidy_table5(p5))
#> # A tibble: 1 × 2
#>   name   data            
#>   <chr>  <list>          
#> 1 table5 <tibble [4 × 9]>

obj1$run(output_dir = dir1, format = "parquet", input_id = "run1")
(lf <- list.files(dir1, pattern = "tool1.*parquet", full.names = FALSE))
#>  [1] "metadata_tool1.parquet"         "sampleA_2_tool1_table1.parquet"
#>  [3] "sampleA_2_tool1_table2.parquet" "sampleA_2_tool1_table3.parquet"
#>  [5] "sampleA_2_tool1_table4.parquet" "sampleA_2_tool1_table6.parquet"
#>  [7] "sampleA_3_tool1_table1.parquet" "sampleA_tool1_table1.parquet"  
#>  [9] "sampleA_tool1_table2.parquet"   "sampleA_tool1_table3.parquet"  
#> [11] "sampleA_tool1_table4.parquet"   "sampleA_tool1_table5.parquet"  
#> [13] "sampleA_tool1_table6.parquet"  

obj2 <- Tool1$new(indir)$tidy()