context("plinkfiles")
test_that("input `plink.raw`", {
data(dat50)
dir <- package.file("inst/extdata/solarAssoc/plink/", package = "solarius")
plink.raw <- file.path(dir, "dat50.raw")
num.snps <- 50
mod <- solarAssoc(trait ~ 1, phenodata, plink.raw = plink.raw)
expect_true(nrow(mod$snpf) == num.snps)
})
test_that("input `plink.raw` and `plink.map`", {
data(dat50)
dir <- package.file("inst/extdata/solarAssoc/plink/", package = "solarius")
plink.raw <- file.path(dir, "dat50.raw")
plink.map <- file.path(dir, "dat50.map")
num.snps <- 50
mod <- solarAssoc(trait ~ 1, phenodata, plink.raw = plink.raw, plink.map = plink.map)
expect_true(nrow(mod$snpf) == num.snps)
expect_true("pos" %in% colnames(mod$snpf))
expect_true(sum(is.na(mod$snpf$pos)) == 0)
})
test_that("input `plink.ped` and `plink.map`", {
data(dat50)
mod0 <- solarAssoc(trait ~ 1, phenodata, snpdata = genodata)
setkey(mod0$snpf, pSNP)
snp.best0 <- mod0$snpf[1, SNP]
# plink format
dir <- package.file("inst/extdata/solarAssoc/plink/", package = "solarius")
plink.ped <- file.path(dir, "dat50.ped")
plink.map <- file.path(dir, "dat50.map")
num.snps <- 50
mod <- solarAssoc(trait ~ 1, phenodata, plink.ped = plink.ped, plink.map = plink.map)
setkey(mod$snpf, pSNP)
snp.best <- mod$snpf[1, SNP]
expect_true(nrow(mod$snpf) == num.snps)
expect_true("pos" %in% colnames(mod$snpf))
expect_true(sum(is.na(mod$snpf$pos)) == 0)
expect_equal(snp.best0, snp.best)
})
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