tests/testthat/test_kingToMatrix.R

In UW-GAC/GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

context("kingToMatrix tests")

test_that("robust", {
	kinfile <- system.file("extdata", "MXL_ASW.kin", package="GENESIS")
	kin0file <- system.file("extdata", "MXL_ASW.kin0", package="GENESIS")
        kin <- read.table(kinfile, header=TRUE, as.is=TRUE)
        kin0 <- read.table(kin0file, header=TRUE, as.is=TRUE)
        samp <- unique(c(kin$ID1, kin$ID2, kin0$ID1, kin0$ID2))

	KINGmat <- kingToMatrix(c(kinfile, kin0file), estimator="Kinship", verbose=FALSE)
        expect_true(setequal(rownames(KINGmat), samp))

        set.seed(5); samp.include <- sample(samp, 100)
	KINGmat <- kingToMatrix(c(kinfile, kin0file), estimator="Kinship", sample.include=samp.include, verbose=FALSE)
        expect_true(setequal(rownames(KINGmat), samp.include))
})

test_that("ibdseg", {
	kinfile <- system.file("extdata", "HapMap.seg", package="GENESIS")
        kin <- read.table(kinfile, header=TRUE, as.is=TRUE)
        samp <- unique(c(kin$ID1, kin$ID2))

	KINGmat <- kingToMatrix(kinfile, verbose=FALSE)
        expect_true(setequal(rownames(KINGmat), samp))
})

test_that("threshold", {
	kinfile <- system.file("extdata", "MXL_ASW.kin", package="GENESIS")
	kin0file <- system.file("extdata", "MXL_ASW.kin0", package="GENESIS")
        kin <- read.table(kinfile, header=TRUE, as.is=TRUE)
	KINGmat <- kingToMatrix(c(kinfile, kin0file), estimator="Kinship", verbose=FALSE)
        rels <- sum(KINGmat > 0)
        
	KINGmat <- kingToMatrix(c(kinfile, kin0file), estimator="Kinship", thresh=0.02, verbose=FALSE)
        rels2 <- sum(KINGmat > 0)
        expect_true(rels2 < rels)
})

test_that("snprelate", {
    gds <- .testData()
    suppressMessages(ibd <- SNPRelate::snpgdsIBDKING(gds, verbose=FALSE))
    KINGmat <- kingToMatrix(ibd, verbose=FALSE)
    expect_true(setequal(rownames(KINGmat), ibd$sample.id))
    seqClose(gds)
})

test_that("wrong column requested", {
    kinfile <- system.file("extdata", "MXL_ASW.kin", package="GENESIS")
    kin0file <- system.file("extdata", "MXL_ASW.kin0", package="GENESIS")
    expect_error(kingToMatrix(c(kinfile, kin0file), verbose=FALSE), "Column PropIBD requested")

    kinfile <- system.file("extdata", "HapMap.seg", package="GENESIS")
    expect_error(kingToMatrix(c(kinfile, kin0file), estimator="Kinship", verbose=FALSE), "Column Kinship requested")
})