testgct.R
context("GCT")
test_that("write.gct and read.gct work", {
load(file = system.file("testdata/GSE27112-GPL6103.rda", package="phantasus"))
gctFile <- tempfile(fileext = ".gct")
write.gct(es, gctFile)
es2 <- read.gct(gctFile)
expect_equal(dim(es2), dim(es))
expect_true(all(colnames(fData(es)) %in% colnames(fData(es2))),
info=setdiff( colnames(fData(es)), colnames(fData(es2))))
expect_true(all(colnames(pData(es)) %in% colnames(pData(es2))),
info=setdiff( colnames(pData(es)), colnames(pData(es2))))
})
test_that("write.gct and read.gct work for gzip files", {
load(file = system.file("testdata/GSE27112-GPL6103.rda", package="phantasus"))
gctFile <- tempfile(fileext = ".gct.gz")
write.gct(es, gctFile, gzip = T)
es2 <- read.gct(gctFile)
expect_equal(dim(es2), dim(es))
})
test_that("read.gct works with duplicate row names", {
expect_warning(es <- read.gct(system.file("testdata/dupl.gct", package="phantasus")))
})