context("Test: DiffGenes() ")
data(PhyloExpressionSetExample)
equal_df <- function(df1, df2) {
rownames(df1) <- NULL
rownames(df2) <- NULL
isTRUE(all.equal(df1, df2))
}
nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]
test_that("is.ExpressionSet() throughs error when no ExpressionSet is entered to DiffGenes()",
{
expect_error(
DiffGenes(
ExpressionSet = nonStandardExpressionSet,
nrep = 2,
comparison = "below",
method = "foldchange",
stage.names = c("S1", "S2", "S3")
)
)
})
test_that("Correct fold change values are computed..", {
set.seed(123)
ExampleMicroarrayTable <-
PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
stage.1 <-
apply(
cbind(ExampleMicroarrayTable[, 3], ExampleMicroarrayTable[, 4]) ,
1 ,
myTAI::geom.mean
)
stage.2 <-
apply(
cbind(ExampleMicroarrayTable[, 5], ExampleMicroarrayTable[, 6]) ,
1 ,
myTAI::geom.mean
)
expect_equal(
DiffGenes(
ExpressionSet = ExampleMicroarrayTable,
nrep = 2,
comparison = "below",
method = "foldchange",
stage.names = c("S1", "S2", "S3")
)[, 3],
stage.1 / stage.2
)
})
test_that("Correct log fold change values are computed..", {
set.seed(123)
ExampleMicroarrayTable <-
PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
stage.1 <-
apply(
cbind(ExampleMicroarrayTable[, 3], ExampleMicroarrayTable[, 4]) ,
1 ,
myTAI::geom.mean
)
stage.2 <-
apply(
cbind(ExampleMicroarrayTable[, 5], ExampleMicroarrayTable[, 6]) ,
1 ,
myTAI::geom.mean
)
expect_equal(
DiffGenes(
ExpressionSet = tf(ExampleMicroarrayTable, log2),
nrep = 2,
comparison = "below",
method = "log-foldchange",
stage.names = c("S1", "S2", "S3")
)[, 3],
log2(stage.1) - log2(stage.2)
)
})
test_that("Correct p-values based on the t-test are computed..", {
set.seed(123)
ExampleMicroarrayTable <-
PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
stage.comp <-
apply(cbind(ExampleMicroarrayTable[, 3:4], ExampleMicroarrayTable[, 5:6]) , 1 , function(x)
t.test(x[1:2], x[3:4])$p.value)
expect_equal(
DiffGenes(
ExpressionSet = ExampleMicroarrayTable,
nrep = 2,
comparison = "below",
method = "t.test",
stage.names = c("S1", "S2", "S3")
)[, 3],
as.numeric(stage.comp)
)
})
test_that("Correct p-values based on the wilcox.test are computed..", {
set.seed(123)
ExampleMicroarrayTable <-
PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
stage.comp <-
apply(cbind(ExampleMicroarrayTable[, 3:4], ExampleMicroarrayTable[, 5:6]) , 1 , function(x)
wilcox.test(x[1:2], x[3:4])$p.value)
expect_equal(
DiffGenes(
ExpressionSet = ExampleMicroarrayTable,
nrep = 2,
comparison = "below",
method = "wilcox.test",
stage.names = c("S1", "S2", "S3")
)[, 3],
as.numeric(stage.comp)
)
})
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