tests/testthat/testGroupClusters.R

In AlexJanse/cMut: Identify Clustered Single Nucleotide Mutations and Link Them to Mutational Patterns

context("Group clusters and show mutation symbols")

testGroupClusters <- groupClusters(identifyClusters(testDataSet,20000,linkPatterns = T),
                                   patternIntersect = T)
validationGroups <- groupClusters(identifyClusters(validationTable,20000,
                                                              sampleIdHeader = "id",
                                                              linkPatterns = T),
                                  patternIntersect = T)
test_that("Check if the patterns match with the expected results",{
          expect_equal(
            testGroupClusters[grepl("TEST",testGroupClusters$clusterId),]$foundPatterns[[1]],
            "AID")
          expect_equal(
            nrow(validationGroups[grepl("AID",validationGroups$foundPatterns),]),
            156/2
          )
          expect_equal(
            nrow(validationGroups[grepl("PolEta",validationGroups$foundPatterns),]),
            8/2
          )
          expect_equal(
            nrow(validationGroups[grepl("A1/A3F",validationGroups$foundPatterns),]),
            44/2
          )
          expect_equal(
            nrow(validationGroups[grepl("A3G",validationGroups$foundPatterns),]),
            12/2
          )
          expect_equal(
            nrow(validationGroups[grepl("A3A",validationGroups$foundPatterns),]),
            8/2
          )
          expect_equal(
            nrow(validationGroups[grepl("A3B",validationGroups$foundPatterns),]),
            8/2
          )
          expect_equal(
            nrow(validationGroups[grepl("A3[^GFAB]",validationGroups$foundPatterns),]),
            32/2
          )
         })

x <- testDataSet
names(x) <- c("chr","pos","endPos","reference","variant","id","sur")
x$sur <- gsub("\\.","-",x$sur)
testPatterns <- mutationPatterns
names(testPatterns) <- c("id","refer","alternative","sur","dist","reference")
data <- identifyClusters(dataTable = x,
                        chromHeader = "chr",
                        positionHeader = "pos",
                        refHeader = "reference",
                        altHeader = "variant",
                        sampleIdHeader = "id",
                        contextHeader = "sur",
                        mutationSymbol = "-",
                        maxDistance = 20000,
                        asTibble = F,
                        linkPatterns = T,
                        reverseComplement = F,
                        searchPatterns = testPatterns,
                        searchAltHeader = "alternative",
                        searchContextHeader = "sur",
                        searchRefHeader = "refer",
                        searchIdHeader = "id",
                        searchDistanceHeader = "dist",
                        searchMutationSymbol = ".",
                        searchReverseComplement = T,
                        linkClustersOnly = T)
names(data)[8] <- "clId"
testGroupClusters2 <- groupClusters(data,
                                   clusterIdHeader = "clId",
                                   refHeader = "reference",
                                   altHeader = "variant",
                                   contextHeader = "sur",
                                   mutationSymbol = "-",
                                   asTibble = F,
                                   searchClusterPatterns = T,
                                   searchPatterns = testPatterns,
                                   searchAltHeader = "alternative",
                                   searchRefHeader = "refer",
                                   searchIdHeader = "id",
                                   searchDistanceHeader = "dist",
                                   searchReverseComplement = T,
                                   patternIntersect = T)
testGroupClusters <- groupClusters(identifyClusters(testDataSet,20000,linkPatterns = T),
                                   patternIntersect = T,
                                   searchClusterPatterns = T,
                                   asTibble = F)

test_that("check if changing the default parameters gives the same result",{
          expect_equal(all(testGroupClusters2[,-c(2,5,9,10)] == testGroupClusters[,-c(2,5,9,10)]),
                       TRUE)
          expect_equal(class(testGroupClusters2),
                       class(data.frame()))
          expect_equal(testGroupClusters[,10][[1]][1],
                       "PolZeta.endOnly")
          expect_equal(nrow(testGroupClusters[testGroupClusters$clusterId == "",]),
                       0)
})

testGroupClusters <- groupClusters(identifyClusters(testDataSet,20000,linkPatterns = T,renameReverse = T),
                                   patternIntersect = T,
                                   searchClusterPatterns = T,
                                   asTibble = F,
                                   renameReverse = T)

test_that("Check if renameReverse works",
          expect_equal(nrow(testGroupClusters[grepl("\\[Rev\\.Com\\.\\]",testGroupClusters$foundPatterns),]),
                       8)
          )