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HRDetect

2023-07-12

Source: vignettes/hrdetect.Rmd
hrdetect.Rmd

Introduction

HRDetect: Homologous Recombination Deficiency Detect (https://github.com/Nik-Zainal-Group/signature.tools.lib)

Data

HRDetect takes as input somatic SNV, INDEL, SV and CNV files. We have made it somewhat easier to feed SNV/INDEL and Manta SV VCFs, together with PURPLE somatic CNV files, with the sigrap::hrdetect_run wrapper.

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")

Analysis 

res <- sigrap::hrdetect_run(
  nm = "sample_A",
  snvindel_vcf = snvindel_vcf,
  sv_vcf = sv_vcf,
  cnv_tsv = cnv_tsv,
  genome = "hg38"
)
#> [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 sample_A.
#> [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: sample_A
#> [info HRDetect_pipeline] HRDetect pipeline completed!

Results 

cbind(var = colnames(res), value = unlist(res[1, ])) |>
  dplyr::as_tibble(.name_repair = "check_unique") |>
  knitr::kable(caption = "HRDetect results.")
HRDetect results.
var value
sample sample_A
Probability 0.806
intercept -3.364
del.mh.prop 6.195
SNV3 2.442
SV3 -0.877
SV5 -1.105
hrdloh_index -1.952
SNV8 0.086

Session Info

Main packages used in this vignette.
package version datestamp source
base 4.2.3 2023-07-12 local
gpgr 1.4.4 2023-07-12 local
signature.tools.lib 2.1.2 2023-07-12 local
sigrap 0.1.1 2023-07-12 local
Platform information.
name value
version R version 4.2.3 (2023-03-15)
os Ubuntu 22.04.2 LTS
system x86_64, linux-gnu
ui X11
language en
collate C.UTF-8
ctype C.UTF-8
tz Etc/UTC
date 2023-07-12
pandoc 2.19.2 @ /usr/share/miniconda/envs/pkgdownenv/bin/ (via rmarkdown)