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 × 11
#> CHROM POS KT AF PURPLE_AF PURPLE_CN PURPLE_MACN PURPLE_VCN SUBCL
#> <chr> <int> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 chr2 45006212 REV_1 0.2143 0.260 1.52 0 0.396 1
#> 2 chr2 45007103 REV_1 0.1977 0.240 1.52 0 0.365 1
#> 3 chr2 45007598 REV_1 0.24 0.291 1.52 0 0.444 1
#> 4 chr2 45007709 REV_1 0.2273 0.276 1.52 0 0.42 1
#> 5 chr3 71010245 REV_2 0.3165 0.405 1.16 0.461 0.469 1
#> 6 chr3 71010553 REV_2 0.1863 0.239 1.16 0.461 0.276 1
#> 7 chr3 71011404 REV_2 0.2841 0.364 1.16 0.461 0.421 1
#> 8 chr3 71011410 REV_2 0.2727 0.349 1.16 0.461 0.405 1
#> 9 chr3 71011474 REV_2 0.2577 0.330 1.16 0.461 0.382 1
#> 10 chr3 71327944 FWD_1 0.1982 0.249 1.26 0.438 0.314 1
#> # ℹ 16 more rows
#> # ℹ 2 more variables: MH <chr>, TNC <chr>
#>
#> $description
#> # A tibble: 9 × 2
#> ID Description
#> <chr> <chr>
#> 1 AF Allele Frequency, for each ALT allele, in the same order as listed
#> 2 KT Forward/reverse kataegis id
#> 3 MH Microhomology
#> 4 PURPLE_AF Purity adjusted allelic frequency of variant
#> 5 PURPLE_CN Purity adjusted copy number surrounding variant location
#> 6 PURPLE_MACN Purity adjusted minor allele ploidy surrounding variant location
#> 7 PURPLE_VCN Purity adjusted ploidy of variant
#> 8 SUBCL Non-zero subclonal likelihood
#> 9 TNC Tri-nucleotide context
#>