tests/testthat/test_GDS.R

In seandavi/GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)

library(GEOquery)
context("GDS")

test_that("generic GDS parsing works as expected", {
  gds <- getGEO(filename = system.file(
    "extdata/GDS507.soft.gz",
    package = "GEOquery"
  ))

  expect_is(gds, "GDS") # gds should be a "GDS"
  expect_is(Meta(gds), "list") # Meta(gds) should be a list
  expect_is(Table(gds), "data.frame") # Table(gds) should be a data.frame
  expect_is(
    dataTable(gds), "GEODataTable"
  ) # dataTable(gds) should be a GEODataTable
  expect_equivalent(nrow(Table(gds)), 22645) # gds has wrong number of rows!
  expect_equivalent(ncol(Table(gds)), 19) # gds has wrong number of columns!
  expect_length(Meta(gds), 23) # gds has wrong number of Metadata entries!
})