Reads the purple.somatic.vcf.gz file.
Value
A list with the input file as a tibble (with specific INFO fields) and a tibble with a description of each INFO field.
Examples
x <- system.file("extdata/purple/purple.somatic.vcf.gz", package = "gpgr")
(snv <- purple_snv_vcf_read(x))
#> $data
#> # A tibble: 423 × 12
#> CHROM POS PURPLE_AF PURPLE_CN PURPLE_GERMLINE PURPLE_MACN PURPLE_VCN
#> <chr> <int> <dbl> <dbl> <chr> <dbl> <dbl>
#> 1 chr1 3086201 0.173 2 NOISE 0.959 0.346
#> 2 chr1 3294434 0.286 2 NOISE 0.959 0.572
#> 3 chr1 3400513 0.136 2 NOISE 0.959 0.272
#> 4 chr1 6957208 0.581 2 NOISE 0.959 1.16
#> 5 chr1 6975198 0.581 2 NOISE 0.959 1.16
#> 6 chr1 7100329 0.596 2 NOISE 0.959 1.19
#> 7 chr1 7185898 0.476 2 NOISE 0.959 0.951
#> 8 chr1 7186176 0.568 2 NOISE 0.959 1.14
#> 9 chr1 7186250 0.741 2 NOISE 0.959 1.48
#> 10 chr1 7290559 0.630 2 NOISE 0.959 1.26
#> # ℹ 413 more rows
#> # ℹ 5 more variables: HMF_HOTSPOT <lgl>, KT <chr>, MH <chr>, SUBCL <dbl>,
#> # TNC <chr>
#>
#> $description
#> # A tibble: 10 × 2
#> ID Description
#> <chr> <chr>
#> 1 HMF_HOTSPOT calculated by flag of overlapping values in field HMF from s…
#> 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_GERMLINE Germline classification surrounding variant location
#> 7 PURPLE_MACN Purity adjusted minor allele ploidy surrounding variant loca…
#> 8 PURPLE_VCN Purity adjusted ploidy of variant
#> 9 SUBCL Non-zero subclonal likelihood
#> 10 TNC Tri-nucleotide context
#>