file <- SNPRelate::snpgdsExampleFileName()
test_that("grange generation works", {
.granges_snpgds <- VariantExperiment:::.granges_snpgds
gr <- .granges_snpgds(file)
expect_s4_class(gr, "GRanges")
expect_s4_class(ranges(gr), "IRanges")
})
test_that("alleles for snpgds works", {
.varnode_snpgds_inmem <- VariantExperiment:::.varnode_snpgds_inmem
res <- .varnode_snpgds_inmem(file, "snp.allele")
expect_s4_class(res$snp.allele1, "DNAStringSet")
expect_s4_class(res$snp.allele2, "DNAStringSet")
expect_equal(dim(res), c(9088L, 2L))
})
test_that("rowRanges works", {
.rowRanges_snpgds <- VariantExperiment:::.rowRanges_snpgds
rr <- .rowRanges_snpgds(file, "snp.id", NULL, TRUE)
expect_s4_class(rr, "GRanges")
expect_s4_class(mcols(rr), "DelayedDataFrame")
expect_equal(names(mcols(rr)), paste0("snp.", c("rs.id", "allele1", "allele2")))
rr <- .rowRanges_snpgds(file, "snp.id", NULL, FALSE)
expect_s4_class(mcols(rr), "DataFrame")
})
test_that("sample related nodes works", {
.colData_snpgds <- VariantExperiment:::.colData_snpgds
res <- .colData_snpgds(file, "sample.id", NULL, TRUE)
expect_s4_class(res, "DelayedDataFrame")
expect_equal(dim(res), c(279L, 5L))
expect_s4_class(res[[1]], "GDSArray")
res <- .colData_snpgds(file, "sample.id", NULL, FALSE)
expect_s4_class(res, "DataFrame")
expect_equal(dim(res), c(279L, 5L))
expect_true(is.character(res[[1]]))
})
test_that("conversion function works", {
ve <- makeVariantExperimentFromSNPGDS(file)
expect_s4_class(ve, "VariantExperiment")
expect_equal(dim(ve), c(9088L, 279L))
expect_s4_class(assay(ve), "DelayedArray")
expect_s4_class(rowData(ve), "DelayedDataFrame")
expect_s4_class(colData(ve), "DelayedDataFrame")
})
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