Zenodo

Each SPN has a dedicated Zenodo record with three zip archives. Files are downloaded once and cached locally — repeat calls skip the download.

Cache location

By default data are stored at ~/.cache/SCOUT/<spn>/. Override with:

Sys.setenv(SCOUT_CACHE_DIR = "/scratch/shared/SCOUT")

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Downloading archives

get_ground_truth()

Downloads ground_truth.zip, reads every RDS file inside, and returns a named list — one element per file.

gt <- get_ground_truth("SPN01")

names(gt)
gt$clones

get_sarek_results()

Downloads sarek.zip and returns the path to the extracted directory.

sarek_dir <- get_sarek_results("SPN01")
list.files(sarek_dir, recursive = TRUE)

get_tumourevo_results()

Downloads tumourevo.zip and returns the path to the extracted directory.

te_dir <- get_tumourevo_results("SPN01")
list.files(te_dir, recursive = TRUE)

list_zenodo_files()

Inspect what is available in a record before downloading anything.

list_zenodo_files("1234567")
#> # A tibble: 3 × 3
#>   filename           size download_url
#>   <chr>             <int> <chr>
#> 1 ground_truth.zip    ...  https://zenodo.org/...
#> 2 sarek.zip           ...  https://zenodo.org/...
#> 3 tumourevo.zip       ...  https://zenodo.org/...

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Ground truth getters

Once get_ground_truth() has been called, these functions let you access specific files without navigating the directory structure manually.

get_mutations()

Returns the path to the mutations RDS file for a given sample type, coverage and purity.

# Tumour sample
path <- get_mutations("SPN01", type = "tumour", coverage = 100, purity = 0.9)
readRDS(path)

# Matched normal (fixed at 30x, purity 1)
path <- get_mutations("SPN01", type = "normal")

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Sarek getters

Once get_sarek_results() has been called, these functions return named lists of file paths for a given sample, coverage, purity and caller.

get_sarek_vcf()

Returns VCF and index file paths. Supported callers: "mutect2", "strelka", "freebayes", "haplotypecaller".

vcf <- get_sarek_vcf("SPN01", "SPN01_1", 100, 0.9, "mutect2", "tumour")
vcf$vcf
vcf$tbi

# strelka returns separate SNV and indel files
vcf <- get_sarek_vcf("SPN01", "SPN01_1", 100, 0.9, "strelka", "tumour")
vcf$snvs_vcf
vcf$indels_vcf

get_sarek_cna()

Returns CNA file paths. Supported callers: "ascat", "sequenza", "cnvkit".

# ASCAT
cna <- get_sarek_cna("SPN01", "SPN01_1", 100, 0.9, "ascat")
cna$segments
cna$purityploidy

# Sequenza
cna <- get_sarek_cna("SPN01", "SPN01_1", 100, 0.9, "sequenza")
cna$segments
cna$confints_CP

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tumourevo getters

Once get_tumourevo_results() has been called, these functions return named lists of file paths. All require spn, coverage, purity, vcf_caller ("mutect2" or "strelka"), and cna_caller ("ascat" or "sequenza").

get_tumourevo_driver()

Driver annotation results for a specific sample.

get_tumourevo_driver("SPN01", 100, 0.9, "mutect2", "ascat", sample = "SPN01_1")

get_tumourevo_subclonal()

Subclonal deconvolution results. Supported tools: "mobster", "pyclonevi", "ctree", "viber".

get_tumourevo_subclonal("SPN01", 100, 0.9, "mutect2", "ascat", "mobster", "SPN01_1")
get_tumourevo_subclonal("SPN01", 100, 0.9, "mutect2", "ascat", "pyclonevi", "SPN01_1")

get_tumourevo_qc()

QC results. Supported tools: "cnaqc", "join_cnaqc", "tinc".

get_tumourevo_qc("SPN01", 100, 0.9, "mutect2", "ascat", "cnaqc", "SPN01_1")

get_tumourevo_signatures()

Signature deconvolution results. Supported tools: "sigprofiler", "sparsesignatures", "BASCULE". sigprofiler also requires a context argument (e.g. "SBS96", "ID83").

# BASCULE
sigs <- get_tumourevo_signatures("SPN01", 100, 0.9, "mutect2", "ascat", "BASCULE")
sigs$refined_fit
sigs$base_fit

# SigProfiler
sigs <- get_tumourevo_signatures("SPN01", 100, 0.9, "mutect2", "ascat",
                                  "sigprofiler", context = "SBS96")
sigs$COSMIC_exposure
sigs$denovo_signatures