gdsfile <- system.file("extdata/test.gds", package = "VariantExperiment")
test_that("grange generation works", {
.granges_generalgds <- VariantExperiment:::.granges_generalgds
gr <- .granges_generalgds(gdsfile, feature.num = 20)
expect_s4_class(gr, "GRanges")
expect_s4_class(ranges(gr), "IRanges")
})
test_that("rowRanges mcols works", {
.rowRanges_generalgds <- VariantExperiment:::.rowRanges_generalgds
rr <- .rowRanges_generalgds(gdsfile, "feature.id", NULL, TRUE)
expect_s4_class(rr, "GRanges")
expect_s4_class(mcols(rr), "DelayedDataFrame")
expect_equal(names(mcols(rr)), c("chromosome", "position"))
rr <- .rowRanges_generalgds(gdsfile, "feature.id", NULL, FALSE)
expect_s4_class(rr, "GRanges")
expect_equal(names(mcols(rr)), c("chromosome", "position"))
expect_s4_class(mcols(rr), "DataFrame")
})
test_that("sample related nodes works", {
.colData_generalgds <- VariantExperiment:::.colData_generalgds
res <- .colData_generalgds(gdsfile, "sample.id", NULL, TRUE)
expect_s4_class(res, "DelayedDataFrame")
expect_equal(dim(res), c(10L, 1L))
expect_s4_class(res[[1]], "GDSArray")
res <- .colData_generalgds(gdsfile, "sample.id", NULL, FALSE)
expect_s4_class(res, "DataFrame")
expect_equal(dim(res), c(10L, 1L))
expect_true(is.character(res[[1]]))
})
test_that("conversion function works", {
ve <- makeVariantExperimentFromGDS(gdsfile, ftnode = "feature.id",
smpnode = "sample.id")
expect_s4_class(ve, "VariantExperiment")
expect_equal(dim(ve), c(20L, 10L))
expect_s4_class(assay(ve), "DelayedMatrix")
})
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