tests/testthat/test_GPL.R

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

library(GEOquery)
context('GPL')

test_that("generic GPL parsing works as expected", {
    gpl = getGEO('GPL96')
    
    expect_is(gpl,'GPL') #gpl is not a GPL object!')
    expect_is(gpl,'GEOData') #gpl does not inherit from GEOData!')
    expect_equivalent(nrow(Table(gpl)),22283) # nrow(gpl) does not match!')
    expect_equivalent(ncol(Table(gpl)),16) #ncol(gpl) does not match!')
    expect_is(Meta(gpl), 'list')  #Meta(gpl) should be a list')
    expect_is(Table(gpl), 'data.frame') #Table(gpl) should be a data.frame')
    expect_is(dataTable(gpl), 'GEODataTable') #dataTable(gpl) should be a GEODataTable')
})

test_that("quoted GPL works", {
    gpl = getGEO('GPL4133')

    expect_equivalent(45220,nrow(Table(gpl))) #GPL4133 should have 45220 rows
})

test_that("short GPL works", {
    gpl = getGEO('GPL15505')
    
    expect_is(gpl,'GPL')
    expect_equivalent(52,nrow(Table(gpl))) #GPL15505 should have 52 rows
})

test_that("GPL with no data table works", {
    gpl = getGEO("GPL5082")
    
    expect_is(gpl,'GPL')
    expect_equivalent(0,nrow(Table(gpl))) #GPL5082 has no data table!
})