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.")| 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
| 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 |
| 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) |