Prepares VCF with SNVs/INDELs for use with HRDetect.
Usage
hrdetect_prep_snvindel(
x,
nm = NULL,
genome = "hg38",
sigsToUse = c(1, 2, 3, 5, 6, 8, 13, 17, 18, 20, 26, 30)
)Arguments
- x
Path to VCF with SNVs and INDELs.
- nm
Sample name.
- genome
Human genome version (default: hg38. hg19 means GRCh37).
- sigsToUse
COSMIC signatures to use.
Value
List with two elements:
snv_results: tibble with exposure score and p-value for chosen signatures.
indel_results: tibble with a summary of the count of indels and their proportion.
Examples
x <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
(l <- hrdetect_prep_snvindel(x, nm = "sampleA"))
#> $snv_results
#> # A tibble: 13 × 2
#> sig exposure
#> <chr> <dbl>
#> 1 Signature1 722.
#> 2 Signature2 0
#> 3 Signature3 1779.
#> 4 Signature5 814.
#> 5 Signature6 0
#> 6 Signature8 1616.
#> 7 Signature13 388.
#> 8 Signature17 0
#> 9 Signature18 0
#> 10 Signature20 0
#> 11 Signature26 0
#> 12 Signature30 0
#> 13 unassigned 625.
#>
#> $indel_results
#> # A tibble: 1 × 12
#> sample del.mh del.rep del.none ins all.indels del.mh.prop del.rep.prop
#> <chr> <int> <int> <int> <int> <int> <dbl> <dbl>
#> 1 sampleA 350 156 109 150 615 0.569 0.254
#> # ℹ 4 more variables: del.none.prop <dbl>, del.mh.count <int>,
#> # del.rep.count <int>, del.none.count <int>
#>