Nothing
context("VCFsToCatalogs function")
test_that("VCFsToCatalogs function for Mutect VCFs", {
skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
files <- list.files(path = "testdata/Mutect-GRCh37", full.names = TRUE)
catalogs1 <- MutectVCFFilesToCatalog(files, ref.genome = "hg19",
region = "genome")
catalogs2 <- MutectVCFFilesToCatalog(files, ref.genome = "hg19",
region = "genome",
return.annotated.vcfs = TRUE)
catalogs3 <- VCFsToCatalogs(files, ref.genome = "hg19",
variant.caller = "mutect", region = "genome")
catalogs4 <- VCFsToCatalogs(files, ref.genome = "hg19",
variant.caller = "mutect", region = "genome",
return.annotated.vcfs = TRUE)
catalogs5 <- VCFsToCatalogs(files, ref.genome = "hg19", region = "genome",
get.vaf.function = GetMutectVAF)
catalogs6 <- VCFsToCatalogs(files, ref.genome = "hg19", region = "genome",
get.vaf.function = GetMutectVAF,
return.annotated.vcfs = TRUE)
expect_equal(catalogs1, catalogs3)
expect_equal(catalogs2, catalogs4)
expect_equal(catalogs1, catalogs5)
expect_equal(catalogs2, catalogs6)
})
test_that("VCFsToCatalogs function for Strelka SBS VCFs", {
skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
files <- list.files(path = "testdata/Strelka-SBS-GRCh37/", full.names = TRUE)
catalogs1 <- StrelkaSBSVCFFilesToCatalog(files, ref.genome = "hg19",
region = "genome")
catalogs2 <- StrelkaSBSVCFFilesToCatalog(files, ref.genome = "hg19",
region = "genome",
return.annotated.vcfs = TRUE)
catalogs3 <- VCFsToCatalogs(files, ref.genome = "hg19",
variant.caller = "strelka", region = "genome")
catalogs4 <- VCFsToCatalogs(files, ref.genome = "hg19",
variant.caller = "strelka", region = "genome",
return.annotated.vcfs = TRUE)
catalogs5 <- VCFsToCatalogs(files, ref.genome = "hg19", region = "genome",
get.vaf.function = GetStrelkaVAF)
catalogs6 <- VCFsToCatalogs(files, ref.genome = "hg19", region = "genome",
get.vaf.function = GetStrelkaVAF,
return.annotated.vcfs = TRUE)
catalogs3$catID <- NULL
expect_equal(catalogs1, catalogs3)
catalogs5$catID <- NULL
expect_equal(catalogs1, catalogs5)
catalogs4$catID <- catalogs4$annotated.vcfs$ID <- NULL
expect_equal(catalogs2, catalogs4)
catalogs6$catID <- catalogs6$annotated.vcfs$ID <- NULL
expect_equal(catalogs2, catalogs6)
})
test_that("VCFsToCatalogs function for Strelka ID VCFs", {
skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
files <- list.files(path = "testdata/Strelka-ID-GRCh37/", full.names = TRUE)
catalogs1 <- StrelkaIDVCFFilesToCatalog(files, ref.genome = "hg19",
region = "genome")
catalogs2 <- StrelkaIDVCFFilesToCatalog(files, ref.genome = "hg19",
region = "genome",
return.annotated.vcfs = TRUE)
catalogs3 <- VCFsToCatalogs(files, ref.genome = "hg19",
variant.caller = "strelka", region = "genome")
catalogs4 <- VCFsToCatalogs(files, ref.genome = "hg19",
variant.caller = "strelka", region = "genome",
return.annotated.vcfs = TRUE)
expect_equal(catalogs1$catalog, catalogs3$catID)
expect_equal(catalogs1$discarded.variants, catalogs3$discarded.variants)
expect_equal(catalogs2$catalog, catalogs4$catID)
expect_equal(catalogs2$discarded.variants, catalogs4$discarded.variants)
expect_equal(catalogs2$annotated.vcfs, catalogs4$annotated.vcfs$ID)
})
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