Nothing
context("Test: MatchMap() ")
data(PhyloExpressionSetExample)
# 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))
}
TestMap <- PhyloExpressionSetExample[c(243,2456,6891,14819,21205), 1:2]
TestExpressionSet <- PhyloExpressionSetExample[ , 2:9]
test_that("MatchMap result matches dplyr::inner_join ",{
MM <- MatchMap(TestMap,TestExpressionSet)
IJ <- dplyr::inner_join(TestMap,TestExpressionSet,by = "GeneID")
expect_true(equal_df(MM[order(MM[ , "GeneID"]), c(1,3:9)],
IJ[order(IJ[ , "GeneID"]), c(1,3:9)]))
expect_true(isTRUE(all.equal.character(as.character(MM[order(MM[ , "GeneID"]), 2]),as.character(IJ[order(IJ[ , "GeneID"]), 2]))))
})
test_that("error occurs when duplicate gene ids are stored in either the PhyloMap or ExpressionSet",{
TestMap2 <- PhyloExpressionSetExample[c(243,2456,243,6891,14819,2456,21205,14819), 1:2]
expect_error(MatchMap(TestMap2,TestExpressionSet),"You have duplicate Gene IDs in your Map. Please enter only unique Gene IDs.")
expect_error(MatchMap(TestMap,PhyloExpressionSetExample[c(243,2456,243,6891,14819,2456,21205,14819), 2:9]),"You have duplicate Gene IDs in your ExpressionMatrix. Please enter only unique Gene IDs, or specify the 'accumulate' argument.")
})
test_that("MatchMap works properly when duplicates are removed via remove.duplicates = TRUE",{
TestMap3 <- PhyloExpressionSetExample[c(243,2456,243,6891,14819,21205,14819), 1:2]
MM <- MatchMap(TestMap3,TestExpressionSet,remove.duplicates = TRUE)
IJ <- dplyr::inner_join(TestMap3[-c(1,5), ],TestExpressionSet,by = "GeneID")
expect_true(equal_df(MM[order(MM[ , "GeneID"]), c(1,3:9)],
IJ[order(IJ[ , "GeneID"]), c(1,3:9)]))
expect_true(isTRUE(all.equal.character(as.character(MM[order(MM[ , "GeneID"]), 2]),as.character(IJ[order(IJ[ , "GeneID"]), 2]))))
})
test_that("MatchMap works properly when duplicates in ExpressionMatrix are accumulated via accumulate = max",{
TestMap <- PhyloExpressionSetExample[c(243,2456,6891,14819,21205), 1:2]
MM <- as.data.frame(MatchMap(TestMap,PhyloExpressionSetExample[c(243,2456,243,6891,14819,21205,14819), 2:9], accumulate = max))
IJ <- dplyr::inner_join(TestMap,TestExpressionSet,by = "GeneID")
expect_true(equal_df(MM[order(MM[ , "GeneID"]), c(1,3:9)],
IJ[order(IJ[ , "GeneID"]), c(1,3:9)]))
expect_true(isTRUE(all.equal.character(as.character(MM[order(MM[ , "GeneID"]), 2]),as.character(IJ[order(IJ[ , "GeneID"]), 2]))))
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.