tests/testthat/test_makeVariantExperimentFromVCF.R

In VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

test_that("makeVariantExperimentFromVCF works", {
    vcf <- SeqArray::seqExampleFileName("vcf")
    ## ve <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile())
    ## ## general
    ## expect_equal(dim(ve), c(1348L, 90L))
    ## expect_equal(dim(rowData(ve)), c(1348L, 14L))
    ## expect_equal(dim(colData(ve)), c(90L, 0L))
    ## expect_s4_class(rowData(ve), "DelayedDataFrame")
    ## expect_s4_class(colData(ve), "DelayedDataFrame")
    ## expect_equal(rownames(rowData(ve)), rownames(ve))
    ## expect_equal(rownames(colData(ve)), colnames(ve))
    ## expect_s4_class(assay(ve,1), "GDSArray")
    
    ## ## contents
    ## expect_equal(names(assays(ve)),
    ##              c("genotype/data", "phase/data", "annotation/format/DP/data"))
    ## expect_equal(colnames(rowData(ve)),
    ##              c("ID", "ALT", "REF", "QUAL", "FILTER", "info_AA", "info_AC",
    ##                "info_AN", "info_DP", "info_HM2", "info_HM3", "info_OR",
    ##                "info_GP", "info_BN" ))
    ## expect_equal(colnames(colData(ve)), character(0))

    ## ## arguments
    ## ve1 <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile(), info.import=c("OR", "GP")) 
    ## expect_equal(colnames(rowData(ve1)),
    ##              c("ID", "ALT", "REF", "QUAL", "FILTER", "info_OR", "info_GP")) 

    ## ve2 <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile(), fmt.import="xx")
    ## expect_equivalent(ve, ve2)
    ## ve3 <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile(), fmt.import=NULL)
    ## expect_equivalent(ve, ve3)
    ## ve4 <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile(), fmt.import="DP")
    ## expect_equivalent(ve, ve4)
    ## ve6 <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile(), reference="hg19")
    ## expect_equivalent(ve, ve6)
    ## ## FIXME: where is the reference info saved in VE? gds attributes? 
    
    ## ve7 <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile(),
    ##                                     start=101, count=1000) 
    ## expect_equal(dim(ve7), c(1000L, 90L))
    ## expect_equal(rownames(ve7), as.character(seq(101, length.out=1000)))


    ## sample.info <- system.file("extdata", "Example_sampleInfo.txt",
    ##                            package="VariantExperiment")
    ## ve8 <- suppressWarnings(
    ##     makeVariantExperimentFromVCF(vcf, out.dir = tempfile(),
    ##                                  sample.info = sample.info))
    ## expect_equal(dim(colData(ve8)), c(90L, 1L))
    ## expect_equal(colnames(colData(ve8)), "family")
    ## ## FIXME: Warning message:
    ## ## In (function (node, name, val = NULL, storage = storage.mode(val),  :
    ## ##   Missing characters are converted to "".
})