tests/testthat/test_getMirSites.R

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

setwd(file.path(getwd(), "testdata"))

context("Test that getMiRsites() function works correctly")
test_that("getMiRsites() generates the correct data structure", {
    gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
    
    # Create the backSplicedJunctions data frame
    backSplicedJunctions <- getBackSplicedJunctions(gtf)
    mergedBSJunctions <- mergeBSJunctions(backSplicedJunctions, gtf)
    
    # Retrive the genomic features
    annotatedBSJs <- annotateBSJs(mergedBSJunctions[9,], gtf)
    
    if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
        # Get BSgenome object
        genome <-
            BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
        
        # Retrieve the target sequences
        targets <- getCircSeqs(annotatedBSJs,
                               gtf,
                               genome)
        
        # miR analysis
        miRsites <- getMiRsites(
            targets,
            miRspeciesCode = "mmu",
            miRBaseLatestRelease = FALSE,
            totalMatches = 7,
            maxNonCanonicalMatches = 0
        )
        
        
        expect_is(miRsites, "list")
        
        namesList <-
            c(
                "targets",
                "microRNAs",
                "counts",
                "totMatchesInSeed",
                "cwcMatchesInSeed",
                "seedLocation",
                "t1",
                "totMatchesInCentral",
                "cwcMatchesInCentral",
                "totMatchesInCompensatory",
                "cwcMatchesInCompensatory",
                "localAUcontent"
            )
        
        expect_equal(names(miRsites), namesList)
        
        expect_equal(length(miRsites), 12)
        
        expect_equal(names(miRsites$targets), .getTargetsColNames())
        expect_equal(names(miRsites$microRNAs),
                     c("id", "length", "seq", "seqRev"))
        
        expect_equal(dim(miRsites$microRNAs)[1], 3)
        expect_equal(miRsites$microRNAs$id,
                     c(">mmu-mySeq", ">mmu-mySeq2", ">mmu-miR-7000-3p"))
    } else{
        cat(
            "Missing package BSgenome.Mmusculus.UCSC.mm10.
            Use BiocManager to install it."
        )
    }
    
    
    
    
})


test_that("getMiRsites() retrieves the correct matches", {
    gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
    # Create the backSplicedJunctions data frame
    backSplicedJunctions <- getBackSplicedJunctions(gtf)
    mergedBSJunctions <- mergeBSJunctions(backSplicedJunctions, gtf)
    
    # Retrive the genomic features
    annotatedBSJs <- annotateBSJs(mergedBSJunctions[11,], gtf)
    
    if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
        # Get BSgenome object
        genome <-
            BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
        
        # Retrieve the target sequences (Arhgap5:+:chr12:52516079:52542636)
        targets <- getCircSeqs(annotatedBSJs,
                               gtf,
                               genome)
        
        
        # We modify the seq so that the miR analysis is faster
        targets$circ$seq <-
            as.character(Biostrings::RNAStringSet(base::substring(targets$circ$seq, 3839, 4089)))
        targets$circ$length <- 200
        
        # miR analysis
        miRsites <- getMiRsites(
            targets,
            miRspeciesCode = "mmu",
            miRBaseLatestRelease = FALSE,
            totalMatches = 7,
            maxNonCanonicalMatches = 0
        )
        
        expect_equal(miRsites$microRNAs$id[1], ">mmu-mySeq")
        expect_equal(miRsites$microRNAs$seqRev[1], "GGUAUACUAGAGCUUCUU")
        
        expect_equal(miRsites$counts[1, 2], 1)
        expect_equal(miRsites$totMatchesInSeed[1, 2], "7")
        expect_equal(miRsites$cwcMatchesInSeed[1, 2], "7mer")
        expect_equal(miRsites$seedLocation[1, 2], "223")
        expect_equal(miRsites$totMatchesInCentral[1, 2], "4")
        expect_equal(miRsites$cwcMatchesInCentral[1, 2], "4")
        expect_equal(miRsites$totMatchesInCompensatory[1, 2], "4")
        expect_equal(miRsites$cwcMatchesInCompensatory[1, 2], "4")
        expect_equal(miRsites$localAUcontent[1, 2], "0.6")
        expect_equal(miRsites$t1[1, 2], "A")
        
        
        
        
        # Retrieve the target sequences (Arhgap5:+:chr12:52516079:52542636)
        targets <- getCircSeqs(annotatedBSJs,
                               gtf,
                               genome)
        
        # We modifie the seq so that the miR analysis is faster
        targets$circ$seq <-
            as.character(Biostrings::RNAStringSet(base::substring(targets$circ$seq, 101, 300)))
        targets$circ$length <- 150
        
        
        # miR analysis
        miRsites <- getMiRsites(
            targets,
            miRspeciesCode = "mmu",
            miRBaseLatestRelease = FALSE,
            totalMatches = 6,
            maxNonCanonicalMatches = 0
        )
        
        expect_equal(miRsites$microRNAs$id[3], ">mmu-miR-7000-3p")
        expect_equal(miRsites$microRNAs$seqRev[3],
                     "GACCUCCUGUCCGUCCACCCAC")
        
        expect_equal(miRsites$counts[1, 4], 1)
        expect_equal(miRsites$totMatchesInSeed[1, 4], "6")
        expect_equal(miRsites$cwcMatchesInSeed[1, 4], "4mer")
        expect_equal(miRsites$seedLocation[1, 4], "160")
        expect_equal(miRsites$totMatchesInCentral[1, 4], "1")
        expect_equal(miRsites$cwcMatchesInCentral[1, 4], "1")
        expect_equal(miRsites$totMatchesInCompensatory[1, 4], "2")
        expect_equal(miRsites$cwcMatchesInCompensatory[1, 4], "1")
        
        expect_equal(miRsites$localAUcontent[1, 4], "0.7")
        expect_equal(miRsites$t1[1, 4], "U")
    } else{
        cat(
            "Missing package BSgenome.Mmusculus.UCSC.mm10.
            Use BiocManager to install it."
        )
    }
    
    
})



test_that(" rearrangeMiRres() rearranges correctly the miRresults", {
    gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
    # Create the backSplicedJunctions data frame
    backSplicedJunctions <- getBackSplicedJunctions(gtf)
    mergedBSJunctions <- mergeBSJunctions(backSplicedJunctions, gtf)
    
    # Retrive the genomic features
    annotatedBSJs <- annotateBSJs(mergedBSJunctions, gtf)
    
    if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
        # Get BSgenome object
        genome <-
            BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
        
        # Retrieve the target sequences
        targets <-
            getCircSeqs(annotatedBSJs[1, ],
                        gtf,
                        genome)
        
        # We only analyze the first row
        miRsites <- getMiRsites(
            targets,
            miRspeciesCode = "mmu",
            miRBaseLatestRelease = FALSE,
            totalMatches = 6,
            maxNonCanonicalMatches = 0
        )
        
        rearrangedMiRres <- rearrangeMiRres(miRsites)
        expect_equal(miRsites$targets$id[1], rearrangedMiRres[[1]][[1]]$id)
        expect_equal(miRsites$targets$length[1], rearrangedMiRres[[1]][[1]]$length)
        expect_equal(miRsites$targets$seq[1], rearrangedMiRres[[1]][[1]]$seq)
        
        col <- 2:ncol(miRsites$counts)
        expect_equal(colnames(miRsites$counts)[col],
                     rearrangedMiRres[[1]][[2]]$miRid)
        expect_equal(as.numeric(miRsites$counts[1, col]),
                     rearrangedMiRres[[1]][[2]]$counts)
        
        expect_equal(as.numeric(miRsites$counts[1, col]),
                     rearrangedMiRres[[1]][[2]]$counts)
        
        expect_equal(
            as.character(miRsites$totMatchesInSeed[1, col]),
            rearrangedMiRres[[1]][[2]]$totMatchesInSeed
        )
        expect_equal(
            as.character(miRsites$cwcMatchesInSeed[1, col]),
            rearrangedMiRres[[1]][[2]]$cwcMatchesInSeed
        )
        expect_equal(as.character(miRsites$seedLocation[1, col]),
                     rearrangedMiRres[[1]][[2]]$seedLocation)
        expect_equal(as.character(miRsites$t1[1, col]), rearrangedMiRres[[1]][[2]]$t1)
        expect_equal(
            as.character(miRsites$totMatchesInCentral[1, col]),
            rearrangedMiRres[[1]][[2]]$totMatchesInCentral
        )
        expect_equal(
            as.character(miRsites$cwcMatchesInCentral[1, col]),
            rearrangedMiRres[[1]][[2]]$cwcMatchesInCentral
        )
        
        expect_equal(
            as.character(miRsites$totMatchesInCompensatory[1, col]),
            rearrangedMiRres[[1]][[2]]$totMatchesInCompensatory
        )
        expect_equal(
            as.character(miRsites$cwcMatchesInCompensatory[1, col]),
            rearrangedMiRres[[1]][[2]]$cwcMatchesInCompensatory
        )
        expect_equal(
            as.character(miRsites$localAUcontent[1, col]),
            rearrangedMiRres[[1]][[2]]$localAUcontent
        )
    } else{
        cat(
            "Missing package BSgenome.Mmusculus.UCSC.mm10.
            Use BiocManager to install it."
        )
    }
    
    
})