inst/unitTests/test_isSNV.R

In VariantAnnotation: Annotation of Genetic Variants

vcf0 <- VCF(rowRanges=GRanges("chr1", IRanges(1:9, width=c(rep(1, 6), 2, 2, 3))), 
            fixed=DataFrame(
              REF=DNAStringSet(c("A", "G", "C", "T", "T", "G", "GG", 
                "TCT", "AC")),
              ALT=DNAStringSetList("G", "A", "T", "C", c("C", "TT"), "GG", 
                "G", "GCG", "ACC")))
str <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
vcf <- readVcf(str, "")

test_isSNV_CollapsedVCF <- function() {
    checkIdentical(isSNV(vcf), logical(nrow(vcf)))
    checkIdentical(isInsertion(vcf), logical(nrow(vcf)))
    target <- c(FALSE, TRUE, rep(FALSE, 5))
    checkIdentical(isDeletion(vcf), target)
    checkIdentical(isIndel(vcf), target)
    checkIdentical(isDelins(vcf), logical(nrow(vcf)))
    checkIdentical(isTransition(vcf), logical(nrow(vcf)))
    checkIdentical(isSubstitution(vcf), logical(nrow(vcf)))

    res1 <- isSNV(vcf0, singleAltOnly=TRUE)
    checkIdentical(res1, c(rep(TRUE, 4), rep(FALSE, 5)))
    res2 <- isSNV(vcf0, singleAltOnly=FALSE)
    checkIdentical(res2, c(rep(TRUE, 5), rep(FALSE, 4)))

    res1 <- isInsertion(vcf0)
    checkIdentical(res1, c(rep(FALSE, 5), TRUE, FALSE, FALSE, FALSE))
    res2 <- isDeletion(vcf0)
    checkIdentical(res2, c(rep(FALSE, 6), TRUE, FALSE, FALSE))
    res3 <- isIndel(vcf0)
    checkIdentical(res3, res1 | res2)
    res4 <- isDelins(vcf0)
    checkIdentical(res4, c(rep(FALSE, 8), TRUE))

    res1 <- isSubstitution(vcf0, singleAltOnly=TRUE)
    checkIdentical(res1, c(rep(TRUE, 4), rep(FALSE, 3), TRUE, FALSE))
    res2 <- isSubstitution(vcf0, singleAltOnly=FALSE)
    checkIdentical(res2, c(rep(TRUE, 5), rep(FALSE, 2), TRUE, FALSE))

    res1 <- isTransition(vcf0, singleAltOnly=TRUE)
    checkIdentical(res1, c(rep(TRUE, 4), rep(FALSE, 5)))
    res2 <- isTransition(vcf0, singleAltOnly=FALSE)
    checkIdentical(res2, c(rep(TRUE, 5), rep(FALSE, 4)))
}

expand <- VariantAnnotation::expand 
test_isSNV_ExpandedVCF <- function() {
    evcf <- expand(vcf)
    checkIdentical(isSNV(evcf), logical(nrow(evcf)))
    checkIdentical(isInsertion(evcf), logical(nrow(evcf)))
    target <- c(FALSE, TRUE, rep(FALSE, 5))
    checkIdentical(isDeletion(evcf), target)
    checkIdentical(isIndel(evcf), target)
    checkIdentical(isDelins(evcf), logical(nrow(evcf)))
    checkIdentical(isTransition(evcf), logical(nrow(evcf)))
    checkIdentical(isSubstitution(evcf), logical(nrow(evcf)))

    evcf0 <- expand(vcf0)
    res <- isSNV(evcf0)
    checkIdentical(sum(res), 5L)

    res1 <- isInsertion(evcf0)
    checkIdentical(sum(res1), 2L)
    res2 <- isDeletion(evcf0)
    checkIdentical(sum(res2), 1L)
    res3 <- isIndel(evcf0)
    checkIdentical(sum(res3), sum(res1 + res2))
    res4 <- isDelins(evcf0)
    checkIdentical(sum(res4), 1L)

    res <- isSubstitution(evcf0)
    checkIdentical(sum(res), 6L)

    res <- isTransition(evcf0)
    checkIdentical(sum(res), 5L)
}

test_isSNV_VRanges <- function() {
    vr <- as(vcf0, "VRanges")

    res <- isSNV(vr)
    checkIdentical(sum(res), 5L)

    res1 <- isInsertion(vr)
    checkIdentical(sum(res1), 2L)
    res2 <- isDeletion(vr)
    checkIdentical(sum(res2), 1L)
    res3 <- isIndel(vr)
    checkIdentical(sum(res3), sum(res1 + res2))
    res4 <- isDelins(vr)
    checkIdentical(sum(res4), 1L)

    res <- isSubstitution(vr)
    checkIdentical(sum(res), 6L)

    res <- isTransition(vr)
    checkIdentical(sum(res), 5L)
}

test_isSNV_gvcf_format <- function() 
{
    ## ignore <NON_REF>
    fl <- system.file("unitTests", "cases", "banded_gvcf.vcf",
                      package="VariantAnnotation")

    vcf <- suppressWarnings(readVcf(fl, ""))
    checkIdentical(isSNV(vcf), c(TRUE, FALSE, TRUE, FALSE, TRUE))
    checkIdentical(isSNV(vcf, singleAltOnly=FALSE), rep(TRUE, nrow(vcf)))
    vr <- as(vcf, "VRanges")
    checkIdentical(isSNV(expand(vcf)), isSNV(vr))
}