Nothing
library(tmod)
context("Testing importing and exporting functions")
data(tmod)
mset <- tmod[c("LI.M37.0", "LI.M75", "LI.M3")]
test_that("MsigDB import", {
fn <- "msigdb_test.xml"
mset <- tmodImportMSigDB(fn)
expect_is(mset, "tmodGS")
expect_output(print(mset), '5 gene sets, 609 genes')
expect_setequal(names(mset), c( "gs", "gs2gv", "gv"))
expect_equal(nrow(mset$gs), length(mset$gs2gv))
})
test_that("working makeTmodFromDataFrame", {
df <- data.frame(gene_id=LETTERS[1:10], geneset_id=rep(letters[2:1], each=5))
mset <- makeTmodFromDataFrame(df)
expect_is(mset, "tmodGS")
expect_output(print(mset), '2 gene sets, 10 genes')
expect_equal(nrow(mset$gs), length(mset$gs2gv))
expect_setequal(names(mset), c( "gs", "gs2gv", "gv"))
mod_a <- getModuleMembers("a", mset)[[1]]
expect_setequal(mod_a, LETTERS[6:10])
})
test_that("tmod2DataFrame works", {
df1 <- tmod2DataFrame(mset)
expect_is(df1, "tbl_df")
expect_equal(nrow(df1), nrow(mset$gs))
df2 <- tmod2DataFrame(mset, rows="features")
expect_equal(nrow(df2), length(mset$gv))
})
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