Run HRDetect via signature.tools.lib

Runs HRDetect as described in the signature.tools.lib repository.

Usage

hrdetect_run(
  nm,
  snvindel_vcf,
  sv_vcf,
  cnv_tsv,
  genome = "hg38",
  sigsToUse = c(1, 2, 3, 5, 6, 8, 13, 17, 18, 20, 26, 30),
  outpath = NULL
)

Arguments

nm

Sample name.

snvindel_vcf

Path to VCF with SNVs and INDELs.

sv_vcf

Path to VCF with SVs.

cnv_tsv

Path to purple.cnv.somatic.tsv file.

genome

Human genome version (default: hg38. hg19 means GRCh37).

sigsToUse

COSMIC SNV signatures to use.

outpath

File to write HRDetect predictions to on disk (should end in '.gz'). If not specified, results won't be written to disk.

Value

Tibble with sample name and HRD probability in first two columns.

Examples

snvindel_vcf <- system.file(
  "extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz",
  package = "gpgr"
)
sv_vcf <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
cnv_tsv <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
nm <- "SampleA"
genome <- "hg38"
(res <- hrdetect_run(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome))
#> [info HRDetect_pipeline] HRDetect pipeline starting!
#> [info HRDetect_pipeline] Single Nucleotide Variations
#> [info HRDetect_pipeline] no SNV catalogues or SNV mutations provided, no signature fit performed.
#> [info HRDetect_pipeline] Structural Variants (Rearrangements)
#> [info HRDetect_pipeline] Running SV signature extraction using the Fit method for samples SampleA.
#> [info signatureFit_pipeline] signatureFit pipeline starting!
#> [info signatureFit_pipeline] no organ provided, so using the reference signatures appropriate for the signature version RefSigv1 and mutation type rearr.
#> [info signatureFit_pipeline] all set, running Fit.
#> [info signatureFit_pipeline] signatureFit pipeline completed!
#> [info HRDetect_pipeline] SV signatures fit completed.
#> [info HRDetect_pipeline] Deletions at Micro-homology (Indels)
#> [info HRDetect_pipeline] HRD-LOH index (CNV)
#> [info HRDetect_pipeline] Computing HRDetect score and feature contributions for the following samples: SampleA
#> [info HRDetect_pipeline] HRDetect pipeline completed!
#> # A tibble: 1 × 9
#>   sample Probability intercept del.mh.prop  SNV3    SV3   SV5 hrdloh_index  SNV8
#>   <chr>        <dbl>     <dbl>       <dbl> <dbl>  <dbl> <dbl>        <dbl> <dbl>
#> 1 Sampl…       0.806     -3.36        6.20  2.44 -0.877 -1.10        -1.95 0.086
# hrdetect_run(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome,
#              outpath = "nogit/hrdetect_results.json.gz")