Reads the purple.purity.tsv
file containing a summary of the purity fit.
Examples
x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
(p <- purple_purity_read(x))
#> $raw
#> # A tibble: 24 × 2
#> column value
#> <chr> <chr>
#> 1 purity 0.75
#> 2 normFactor 1.05
#> 3 score 0.26
#> 4 diploidProportion 0.86
#> 5 ploidy 1.87
#> 6 gender MALE
#> 7 status NORMAL
#> 8 polyclonalProportion 0
#> 9 minPurity 0.71
#> 10 maxPurity 0.78
#> # ℹ 14 more rows
#>
#> $summary
#> # A tibble: 10 × 4
#> n variable value details
#> <dbl> <chr> <glue> <chr>
#> 1 2 Purity 0.75 (0.71-0.78) Purity of tumor in the sample (and mi…
#> 2 3 Ploidy 1.87 (1.86-1.88) Average ploidy of tumor sample after …
#> 3 4 Gender MALE Gender as inferred by AMBER/COBALT.
#> 4 7 WGD FALSE Whole genome duplication (more than 1…
#> 5 8 MSI (indels/Mb) MSS (0) MSI status (MSI, MSS or UNKNOWN if so…
#> 6 9 PolyclonalProp 0 Proportion of CN regions that are mor…
#> 7 10 DiploidyProp 0.86 (0.86-0.86) Proportion of CN regions that have 1 …
#> 8 11 TMB 0 (LOW) Tumor mutational burden (# PASS varia…
#> 9 12 TML 0 (LOW) Tumor mutational load (# of missense …
#> 10 13 TMB-SV 713 # of non inferred, non single passing…
#>