tests/testthat/testHypergeometricTest.R
In koralgooll/MulEA: MulEA - A Tool for Multi Enrichment Analysis
test_that("ora : object creation test.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "c")
poolMock <- c("a", "c", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
testthat::expect_equal(mulea_ora_model@gmt, gmtMock)
testthat::expect_equal(mulea_ora_model@element_names, c("a", "b", "c"))
testthat::expect_equal(mulea_ora_model@background_element_names, c("a", "c", "d"))
testthat::expect_equal(mulea_ora_model@p_value_adjustment_method, "eFDR")
})
test_that("ora : object creation test : adjustment type.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "c")
poolMock <- c("a", "c", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "BH",
number_of_cpu_threads = 2)
testthat::expect_equal(mulea_ora_model@p_value_adjustment_method, "BH")
})
test_that("ora : element_names out of DB model.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2
)
testthat::expect_warning(muleaTestRes <- run_test(mulea_ora_model))
testthat::expect_equal(muleaTestRes$p_value, 1)
})
test_that("ora : element_names out of pool.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "c")
poolMock <- c("a", "b", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
testthat::expect_warning(muleaTestRes <- run_test(mulea_ora_model))
testthat::expect_equal(muleaTestRes$p_value, 1 / 3)
})
test_that("ora : matrix 2,2,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "c", "d", "e", "f", "g", "h")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, 53 / 70)
})
test_that("ora : pool >> var + DBi, matrix 2,2,2,18.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <-
c(
"a",
"b",
"c",
"d",
"e",
"f",
"g",
"h",
"i",
"j",
"k",
"l",
"m",
"n",
"o",
"p",
"q",
"r",
"s",
"t",
"u",
"w",
"x",
"y"
)
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, 37 / 322)
})
test_that("ora : DBi not include pool, matrix 2,0,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "e", "f", "g", "h")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, 0.4)
})
test_that("ora : DB1 + DB2 => pool, matrix 1,3,2,2 and 2,2,1,3.", {
gmtMock1 <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
gmtMock2 <- data.frame(
ontologyId = "GO:0000002",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("e", "f", "g", "h"))),
stringsAsFactors = FALSE
)
gmtMock <- rbind(gmtMock1, gmtMock2)
testDataMock <- c("d", "e", "f")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2
)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, c(13 / 14, 0.5))
})
test_that("ora : DB1 + DB2 => pool, matrix 2,2,2,0 and 2,2,1,3.", {
gmtMock1 <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
gmtMock2 <- data.frame(
ontologyId = "GO:0000002",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("e", "f", "c", "d"))),
stringsAsFactors = FALSE
)
gmtMock <- rbind(gmtMock1, gmtMock2)
testDataMock <- c("b", "d", "e", "f")
poolMock <-
c(
"a",
"b",
"c",
"d",
"e",
"f",
"g",
"h",
"i",
"j",
"k",
"l",
"m",
"n",
"o",
"p",
"q",
"r",
"s",
"t",
"u",
"w",
"x",
"y"
)
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, c(37 / 322, 27 / 3542))
})
test_that("ora : DB1 + DB2 => pool, matrix 2,2,2,0 and 2,2,1,3.", {
gmtMock <- read_gmt(file = system.file(package="MulEA", "extdata", "model.gmt"))
testDataMock <- c("FBgn0004407", "FBgn0010438", "FBgn0037044", "FBgn0002887", "FBgn0028434", "FBgn0030170", "FBgn0263831")
poolMock <- unique(c(c("FBgn0033690", "FBgn0261618", "FBgn0004407", "FBgn0010438", "FBgn0032154", "FBgn0039930", "FBgn0040268", "FBgn0013674",
"FBgn0037008", "FBgn0003116", "FBgn0037743", "FBgn0035401", "FBgn0037044", "FBgn0051005", "FBgn0026737", "FBgn0026751",
"FBgn0038704", "FBgn0002887", "FBgn0028434", "FBgn0030170", "FBgn0263831", "FBgn0000579"),
c("FBgn0066666", "FBgn0000000", "FBgn0099999", "FBgn0011111", "FBgn0022222", "FBgn0777777", "FBgn0333333")))
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names=poolMock,
number_of_cpu_threads = 2
)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value[c(1,2)], c(1, 19205/26423))
})
test_that("ora : private : matrix 2,2,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "c", "d", "e", "f", "g", "h")
mulea_hyper_test <- MulEA:::MuleaHypergeometricTest(
gmt = gmtMock,
element_names = testDataMock,
pool = poolMock,
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_hyper_test)
testthat::expect_equal(muleaTestRes$p.value, 53 / 70)
})
test_that("ora : private : DBi not include pool, matrix 2,0,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "e", "f", "g", "h")
mulea_hyper_test <- MulEA:::MuleaHypergeometricTest(
gmt = gmtMock,
element_names = testDataMock,
pool = poolMock,
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_hyper_test)
testthat::expect_equal(muleaTestRes$p.value, 0.4)
})
koralgooll/MulEA documentation built on Nov. 23, 2023, 3:27 p.m.
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test_that("ora : object creation test.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "c")
poolMock <- c("a", "c", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
testthat::expect_equal(mulea_ora_model@gmt, gmtMock)
testthat::expect_equal(mulea_ora_model@element_names, c("a", "b", "c"))
testthat::expect_equal(mulea_ora_model@background_element_names, c("a", "c", "d"))
testthat::expect_equal(mulea_ora_model@p_value_adjustment_method, "eFDR")
})
test_that("ora : object creation test : adjustment type.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "c")
poolMock <- c("a", "c", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "BH",
number_of_cpu_threads = 2)
testthat::expect_equal(mulea_ora_model@p_value_adjustment_method, "BH")
})
test_that("ora : element_names out of DB model.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2
)
testthat::expect_warning(muleaTestRes <- run_test(mulea_ora_model))
testthat::expect_equal(muleaTestRes$p_value, 1)
})
test_that("ora : element_names out of pool.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "c")
poolMock <- c("a", "b", "d")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
testthat::expect_warning(muleaTestRes <- run_test(mulea_ora_model))
testthat::expect_equal(muleaTestRes$p_value, 1 / 3)
})
test_that("ora : matrix 2,2,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "c", "d", "e", "f", "g", "h")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, 53 / 70)
})
test_that("ora : pool >> var + DBi, matrix 2,2,2,18.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <-
c(
"a",
"b",
"c",
"d",
"e",
"f",
"g",
"h",
"i",
"j",
"k",
"l",
"m",
"n",
"o",
"p",
"q",
"r",
"s",
"t",
"u",
"w",
"x",
"y"
)
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, 37 / 322)
})
test_that("ora : DBi not include pool, matrix 2,0,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "e", "f", "g", "h")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, 0.4)
})
test_that("ora : DB1 + DB2 => pool, matrix 1,3,2,2 and 2,2,1,3.", {
gmtMock1 <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
gmtMock2 <- data.frame(
ontologyId = "GO:0000002",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("e", "f", "g", "h"))),
stringsAsFactors = FALSE
)
gmtMock <- rbind(gmtMock1, gmtMock2)
testDataMock <- c("d", "e", "f")
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2
)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, c(13 / 14, 0.5))
})
test_that("ora : DB1 + DB2 => pool, matrix 2,2,2,0 and 2,2,1,3.", {
gmtMock1 <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
gmtMock2 <- data.frame(
ontologyId = "GO:0000002",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("e", "f", "c", "d"))),
stringsAsFactors = FALSE
)
gmtMock <- rbind(gmtMock1, gmtMock2)
testDataMock <- c("b", "d", "e", "f")
poolMock <-
c(
"a",
"b",
"c",
"d",
"e",
"f",
"g",
"h",
"i",
"j",
"k",
"l",
"m",
"n",
"o",
"p",
"q",
"r",
"s",
"t",
"u",
"w",
"x",
"y"
)
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names = poolMock,
p_value_adjustment_method = "eFDR",
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value, c(37 / 322, 27 / 3542))
})
test_that("ora : DB1 + DB2 => pool, matrix 2,2,2,0 and 2,2,1,3.", {
gmtMock <- read_gmt(file = system.file(package="MulEA", "extdata", "model.gmt"))
testDataMock <- c("FBgn0004407", "FBgn0010438", "FBgn0037044", "FBgn0002887", "FBgn0028434", "FBgn0030170", "FBgn0263831")
poolMock <- unique(c(c("FBgn0033690", "FBgn0261618", "FBgn0004407", "FBgn0010438", "FBgn0032154", "FBgn0039930", "FBgn0040268", "FBgn0013674",
"FBgn0037008", "FBgn0003116", "FBgn0037743", "FBgn0035401", "FBgn0037044", "FBgn0051005", "FBgn0026737", "FBgn0026751",
"FBgn0038704", "FBgn0002887", "FBgn0028434", "FBgn0030170", "FBgn0263831", "FBgn0000579"),
c("FBgn0066666", "FBgn0000000", "FBgn0099999", "FBgn0011111", "FBgn0022222", "FBgn0777777", "FBgn0333333")))
mulea_ora_model <- MulEA::ora(
gmt = gmtMock,
element_names = testDataMock,
background_element_names=poolMock,
number_of_cpu_threads = 2
)
muleaTestRes <- run_test(mulea_ora_model)
testthat::expect_equal(muleaTestRes$p_value[c(1,2)], c(1, 19205/26423))
})
test_that("ora : private : matrix 2,2,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "c", "d", "e", "f", "g", "h")
mulea_hyper_test <- MulEA:::MuleaHypergeometricTest(
gmt = gmtMock,
element_names = testDataMock,
pool = poolMock,
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_hyper_test)
testthat::expect_equal(muleaTestRes$p.value, 53 / 70)
})
test_that("ora : private : DBi not include pool, matrix 2,0,2,2.", {
gmtMock <- data.frame(
ontologyId = "GO:0000001",
ontologyName = "Imagin gen ontology to tests.",
listOfValues = I(list(c("a", "b", "c", "d"))),
stringsAsFactors = FALSE
)
testDataMock <- c("a", "b", "e", "f")
poolMock <- c("a", "b", "e", "f", "g", "h")
mulea_hyper_test <- MulEA:::MuleaHypergeometricTest(
gmt = gmtMock,
element_names = testDataMock,
pool = poolMock,
number_of_cpu_threads = 2)
muleaTestRes <- run_test(mulea_hyper_test)
testthat::expect_equal(muleaTestRes$p.value, 0.4)
})
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