Nothing
context("Loading ENCODE data")
data("ENCODEmetadata")
data("counts")
test_that("Load ENCODE gene expression for EIF4G1", {
expect_is(ENCODEmetadata, "tbl_df")
expect_identical(ENCODEmetadata$`Experiment target`, rep("EIF4G1", 2))
expect_identical(colnames(counts),
c("gene_id", "transcript_id(s)",
paste0("shRNA", 1:2), paste0("control", 1:2)))
})
test_that("Download ENCODE knockdown metadata", {
skip_on_bioc()
metadata <- downloadENCODEknockdownMetadata("HepG2", "EIF4G1")
expect_equal(nrow(metadata), 2)
expect_equal(unique(metadata$`File format`), "tsv")
expect_equal(unique(metadata$`Output type`), "gene quantifications")
expect_equal(unique(metadata$Assay), "shRNA RNA-seq")
expect_equal(unique(metadata$`Biosample term name`), "HepG2")
expect_equal(unique(metadata$`Biosample genetic modifications categories`),
"interference")
expect_equal(unique(metadata$`Biosample genetic modifications methods`),
"RNAi")
expect_equal(unique(metadata$`Experiment target`), "EIF4G1")
expect_equal(unique(metadata$`Library made from`), "polyadenylated mRNA")
expect_equal(unique(metadata$Project), "ENCODE")
expect_equal(unique(metadata$`Biological replicate(s)`), c("1", "2"))
expect_equal(unique(metadata$`File assembly`), "hg19")
expect_equal(unique(metadata$`File Status`), "released")
})
# test_that("Perform differential gene expression", {
# data("ENCODEsamples")
# counts <- prepareENCODEgeneExpression(ENCODEsamples)
#
# diffExpr <- performDifferentialExpression(counts)
# expect_is(diffExpr, "data.frame")
# expect_identical(colnames(diffExpr), c("Gene_symbol", "logFC", "AveExpr",
# "t", "P.Value", "adj.P.Val", "B"))
# })
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