tests/testthat/test_DataObj.R

In CshlSiepelLab/ACE: Analysis of CRISPR Essentiality in R

context('Testing DataObj object.')
library(ACER)
setup({
  write.table(data.table('guide' = paste0('g', 1:3),
                         'gene' = 'gene1',
                         'init_1' = c(0,1,1),
                         'dep_1' = c(0,2,3)),
              quote = F, row.names = F,
              file = 'test_CountOne.txt')
  write.table(data.table('sgrna' = paste0('g', 1:3),
                         'count' = c(0,300,300)),
              file = 'test_MasterOne.txt',
              quote = F, row.names = F)
  write.table(data.table('sgrna' = paste0('g', 1:3),
                         'gene' = 'gene1',
                         'dep_1' = c(0,3,3),
                         'dep_2' = c(0, 50, 50)),
              row.names = F, quote = F,
              file = 'test_CountOneDep.txt')
  write.table(data.table('guide' = paste0('g', 1:3),
                         'gene' = 'gene1',
                         'init_1' = rep(0,3),
                         'dep_1' = rep(0,3)), row.names = F,
              file = 'test_CountNull.txt')
  write.table(data.table('sgrna' = paste0('g', 1:3),
                         'count' = rep(0,3)),
              file = 'test_MasterNull.txt', row.names = F)
  write.table(data.table('guide' = paste0('g', 1:3),
                         'gene' = 'gene1',
                         'init_1' = c(2,2,2),
                         'dep_1' = c(1,1,1),
                         'init2' = c(3,0,3),
                         'dep_2' = c(2,0,2)),
              file = 'test_DropSample.txt', row.names = F)
  write(x='Debugging Messages from DataObj Class',
        file = 'DataObj_debugger.txt')
  write.table(data.table('guide' = paste0('g', 1:3),
                         'gene' = 'gene1',
                         'dep_1' = c(0,2,3),
                         'dep_2' = c(0,4,5)),
              row.names = F,
              file = 'testZeroCountsInOne.txt')
  write.table(data.table('sgrna' = paste0('g', 1:3),
                         'count' = c(200,300,300)),
              file = 'testMaster.txt', row.names = F)
  write.table(data.table('sgrna' = paste0('g', 1:3),
                         'count' = c(2000,3000,3000)),
              file = 'testMaster2.txt', row.names = F)
  write.table(data.table('sample' = c('dep_1', 'dep_2'),
                         'masterlib_file' = c('testMaster2.txt', 
                                              'testMaster.txt')),
              col.names = T, row.names=F,
              file = 'testMasterInfo.txt')
})

teardown({
  file.remove('test_CountOne.txt',
              'test_MasterOne.txt',
              'test_CountOneDep.txt',
              'test_CountNull.txt',
              'test_MasterNull.txt',
              'test_DropSample.txt',
              'testMaster.txt',
              'testMaster2.txt',
              'testZeroCountsInOne.txt',
              'testMasterInfo.txt')

  file.remove(sapply(dir('ACE_output_data'),function(f) {
    file.path('ACE_output_data', f)}))
  file.remove('DataObj_debugger.txt')
})

test_that('Test no counts in any gene in any sample throws an error.', {

  expect_error(capture_warnings(DataObj$new(masterFiles = c('test_MasterNull.txt'),
                                countFile = 'test_CountNull.txt')),
               'No valid data submitted.')
})
test_that('Blank guides should be removed from count data with a warning.', {

  warnAll <- capture_warnings(testDataObjAll <- DataObj$new(masterFiles = c('test_MasterOne.txt'),
                                              countFile = 'test_CountOne.txt'))
  write(warnAll, file = 'DataObj_debugger.txt', append=T)

  warnMaster <- capture_warnings(testDataObjMaster <- DataObj$new(masterFiles = c('test_MasterOne.txt'),
                                                                  countFile = 'test_CountOneDep.txt',
                                                                  hasInitSeq = F))
  write(warnMaster, file = 'DataObj_debugger.txt', append=T)
  warnInit <- capture_warnings(testDataObjInit <- DataObj$new(countFile = 'test_CountOne.txt'))
  write(warnInit, file = 'DataObj_debugger.txt', append=T)

  expect_equal(2, nrow(testDataObjAll$dep_counts))
  expect_equal(2, nrow(testDataObjMaster$dep_counts))
  expect_equal(2, nrow(testDataObjInit$dep_counts))

  checkData <- debugData(testDataObjAll, printAll = F)
  expect_equal(0, length(checkData$flag))
  expect_equal(length(testDataObjAll$init_total_reads), 1)
})

test_that('Test guides missing from only one sample are included.', {

  testDataObj <- DataObj$new(countFile = 'test_DropSample.txt',
                            hasInitSeq = T)
  # 2 samples, 3 guides; all should be present.
  expect_equal(dim(testDataObj$dep_counts), c(3,2))
})

test_that('Create DataObj with multiple masterlibraries, no init seq.', {
  # No sample-masterlib mapping, but multiple master libraries.
  # ACE requires masterlibrary replicates as single table.
  expect_error(testDataObj <- DataObj$new(masterFiles = c('testMaster.txt',
                                             'testMaster2.txt'),
                             countFile = 'testZeroCountsInOne.txt',
                             hasInitSeq = F),
               "please provide assignment of master libraries to samples")
  # Sample-masterlib mapping provided.
  expect_message(testDataObj2 <- DataObj$new(masterFiles = c('testMaster.txt',
                                                            'testMaster2.txt'),
                                            countFile = 'testZeroCountsInOne.txt',
                                            hasInitSeq = F,
                                            sampleMasterInfoFile = 'testMasterInfo.txt'))
  expect_equal(length(testDataObj2$master_counts),2)
})