Nothing
context("Test: CollapseReplicates() ")
# adapted from: https://github.com/hadley/dplyr/blob/master/tests/testthat/test-arrange.r
equal_df <- function(df1, df2) {
rownames(df1) <- NULL
rownames(df2) <- NULL
isTRUE(all.equal(df1, df2))
}
data(PhyloExpressionSetExample)
# test df: mean, nrep = 2, stage.names = c("S1","S2","S3")
TestCollapsedDF1 <-
cbind(
PhyloExpressionSetExample[1:5, 1:2],
apply(PhyloExpressionSetExample[1:5, 3:4], 1, mean),
apply(PhyloExpressionSetExample[1:5, 5:6], 1, mean),
apply(PhyloExpressionSetExample[1:5, 7:8], 1, mean)
)
colnames(TestCollapsedDF1)[3:5] <- c("S1", "S2", "S3")
# test df: mean, nrep = c(2,2,3), stage.names = c("S1","S2","S3")
TestCollapsedDF2 <-
cbind(
PhyloExpressionSetExample[1:5, 1:2],
apply(PhyloExpressionSetExample[1:5, 3:4], 1, mean),
apply(PhyloExpressionSetExample[1:5, 5:6], 1, mean),
apply(PhyloExpressionSetExample[1:5, 7:9], 1, mean)
)
colnames(TestCollapsedDF2)[3:5] <- c("S1", "S2", "S3")
# test df: median, nrep = 2, stage.names = c("S1","S2","S3")
TestCollapsedDF3 <-
cbind(
PhyloExpressionSetExample[1:5, 1:2],
apply(PhyloExpressionSetExample[1:5, 3:4], 1, median),
apply(PhyloExpressionSetExample[1:5, 5:6], 1, median),
apply(PhyloExpressionSetExample[1:5, 7:8], 1, median)
)
colnames(TestCollapsedDF3)[3:5] <- c("S1", "S2", "S3")
# test df: max, nrep = 2, stage.names = c("S1","S2","S3")
TestCollapsedDF4 <-
cbind(
PhyloExpressionSetExample[1:5, 1:2],
apply(PhyloExpressionSetExample[1:5, 3:4], 1, max),
apply(PhyloExpressionSetExample[1:5, 5:6], 1, max),
apply(PhyloExpressionSetExample[1:5, 7:8], 1, max)
)
colnames(TestCollapsedDF4)[3:5] <- c("S1", "S2", "S3")
# test df: median, nrep = c(2,2,3), stage.names = c("S1","S2","S3")
TestCollapsedDF5 <-
cbind(
PhyloExpressionSetExample[1:5, 1:2],
apply(PhyloExpressionSetExample[1:5, 3:4], 1, median),
apply(PhyloExpressionSetExample[1:5, 5:6], 1, median),
apply(PhyloExpressionSetExample[1:5, 7:9], 1, median)
)
colnames(TestCollapsedDF5)[3:5] <- c("S1", "S2", "S3")
# test df: max, nrep = c(2,2,3), stage.names = c("S1","S2","S3")
TestCollapsedDF6 <-
cbind(
PhyloExpressionSetExample[1:5, 1:2],
apply(PhyloExpressionSetExample[1:5, 3:4], 1, max),
apply(PhyloExpressionSetExample[1:5, 5:6], 1, max),
apply(PhyloExpressionSetExample[1:5, 7:9], 1, max)
)
colnames(TestCollapsedDF6)[3:5] <- c("S1", "S2", "S3")
test_that("CollapseReplicates() works with const. nrep = 2 and FUN = mean", {
expect_true(equal_df(
CollapseReplicates(
PhyloExpressionSetExample[1:5, 1:8],
2,
mean,
c("S1", "S2", "S3")
),
TestCollapsedDF1
))
})
test_that("CollapseReplicates() works with const. nrep = 2 and FUN = 'mean' (quoted)",
{
expect_true(equal_df(
CollapseReplicates(
PhyloExpressionSetExample[1:5, 1:8],
2,
"mean",
c("S1", "S2", "S3")
),
TestCollapsedDF1
))
})
test_that("CollapseReplicates() works with const. nrep = 2 and FUN = median", {
expect_true(equal_df(
CollapseReplicates(
PhyloExpressionSetExample[1:5, 1:8],
2,
median,
c("S1", "S2", "S3")
),
TestCollapsedDF3
))
})
test_that("CollapseReplicates() works with const. nrep = 2 and FUN = max", {
expect_true(equal_df(
CollapseReplicates(PhyloExpressionSetExample[1:5, 1:8], 2, max, c("S1", "S2", "S3")),
TestCollapsedDF4
))
})
test_that("CollapseReplicates() works with variable nrep = c(2,2,3) and FUN = mean",
{
expect_true(equal_df(
CollapseReplicates(
PhyloExpressionSetExample[1:5, 1:9],
c(2, 2, 3),
mean,
c("S1", "S2", "S3")
),
TestCollapsedDF2
))
})
test_that("CollapseReplicates() works with variable nrep = c(2,2,3) and FUN = median",
{
expect_true(equal_df(
CollapseReplicates(
PhyloExpressionSetExample[1:5, 1:9],
c(2, 2, 3),
median,
c("S1", "S2", "S3")
),
TestCollapsedDF5
))
})
test_that("CollapseReplicates() works with variable nrep = c(2,2,3) and FUN = max",
{
expect_true(equal_df(
CollapseReplicates(
PhyloExpressionSetExample[1:5, 1:9],
c(2, 2, 3),
max,
c("S1", "S2", "S3")
),
TestCollapsedDF6
))
})
nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]
test_that(
"is.ExpressionSet() throughs error when no ExpressionSet is entered to CollapseReplicates()",
{
expect_error(
CollapseReplicates(nonStandardExpressionSet, 2, mean)
)
}
)
TestCollapsedDF_stage.names <- TestCollapsedDF1
colnames(TestCollapsedDF_stage.names)[3:5] <- paste0("X", 1:3)
test_that("default stage.names work properly when stage.names = NULL", {
expect_true(equal_df(
CollapseReplicates(PhyloExpressionSetExample[1:5, 1:8], 2, mean),
TestCollapsedDF_stage.names
))
})
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