Reads the purple.somatic.vcf.gz file and extracts variants
within kataegis regions.
Value
A list with a tibble containing variants in kataegis clusters and various metrics for each variant, and a tibble with a description of each metric.
Examples
x <- system.file("extdata/purple/purple.somatic.vcf.gz", package = "gpgr")
(k <- purple_kataegis(x))
#> $data
#> # A tibble: 26 × 10
#> CHROM POS KT PURPLE_AF PURPLE_CN PURPLE_MACN PURPLE_VCN SUBCL MH
#> <chr> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 chr2 45006212 REV_1 0.260 1.52 0 0.396 1 NA
#> 2 chr2 45007103 REV_1 0.240 1.52 0 0.365 1 NA
#> 3 chr2 45007598 REV_1 0.291 1.52 0 0.444 1 NA
#> 4 chr2 45007709 REV_1 0.276 1.52 0 0.42 1 NA
#> 5 chr3 71010245 REV_2 0.405 1.16 0.461 0.469 1 NA
#> 6 chr3 71010553 REV_2 0.239 1.16 0.461 0.276 1 NA
#> 7 chr3 71011404 REV_2 0.364 1.16 0.461 0.421 1 NA
#> 8 chr3 71011410 REV_2 0.349 1.16 0.461 0.405 1 NA
#> 9 chr3 71011474 REV_2 0.330 1.16 0.461 0.382 1 NA
#> 10 chr3 71327944 FWD_1 0.249 1.26 0.438 0.314 1 NA
#> # ℹ 16 more rows
#> # ℹ 1 more variable: TNC <chr>
#>
#> $description
#> # A tibble: 8 × 2
#> ID Description
#> <chr> <chr>
#> 1 KT Forward/reverse kataegis id
#> 2 MH Microhomology
#> 3 PURPLE_AF Purity adjusted allelic frequency of variant
#> 4 PURPLE_CN Purity adjusted copy number surrounding variant location
#> 5 PURPLE_MACN Purity adjusted minor allele ploidy surrounding variant location
#> 6 PURPLE_VCN Purity adjusted ploidy of variant
#> 7 SUBCL Non-zero subclonal likelihood
#> 8 TNC Tri-nucleotide context
#>