Read PURPLE Purity file — purple_purity

Reads the purple.purity.tsv file containing a summary of the purity fit.

Usage

purple_purity_read(x)

Arguments

x: Path to the purple.purity.tsv file.

Value

The input file as a tibble and a summarised tibble with a description of each metric.

Examples

x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
(p <- purple_purity_read(x))
#> $raw
#> # A tibble: 25 × 2
#>    column               value 
#>    <chr>                <chr> 
#>  1 purity               0.99  
#>  2 normFactor           0.71  
#>  3 score                1.06  
#>  4 diploidProportion    0.03  
#>  5 ploidy               2.86  
#>  6 gender               MALE  
#>  7 status               NORMAL
#>  8 polyclonalProportion 0.13  
#>  9 minPurity            0.98  
#> 10 maxPurity            1     
#> # ℹ 15 more rows
#> 
#> $summary
#> # A tibble: 9 × 4
#>       n variable       value            details                                 
#>   <dbl> <chr>          <glue>           <chr>                                   
#> 1     2 Purity         0.99 (0.98-1)    Purity of tumor in the sample (and min-…
#> 2     3 Ploidy         2.86 (2.78-2.94) Average ploidy of tumor sample after ad…
#> 3     4 Gender         MALE             Gender as inferred by AMBER/COBALT.     
#> 4     7 WGD            TRUE             Whole genome duplication (more than 10 …
#> 5     8 PolyclonalProp 0.13             Proportion of CN regions that are more …
#> 6     9 DiploidyProp   0.03 (0.02-0.04) Proportion of CN regions that have 1 (+…
#> 7    10 TMB            15.13 (HIGH)     Tumor mutational burden (# PASS variant…
#> 8    11 TML            349 (HIGH)       Tumor mutational load (# of missense va…
#> 9    12 TMB-SV         1267             # of non inferred, non single passing S…
#>