Nothing
context("snpmap")
# input data
test_that("3 snps, 2 snps in map", {
data(dat50)
snpind <- 1:3
snpind.map <- 1:2
mod <- solarAssoc(trait ~ 1, phenodata, snpdata = genodata, snpind = snpind, snpmap = snpdata[snpind.map, ])
expect_equal(nrow(mod$snpf), length(snpind))
expect_true("pos" %in% colnames(mod$snpf))
expect_true(sum(!is.na(mod$snpf$pos)) == length(snpind.map))
})
test_that("1 `genocov.files`", {
data(dat50)
dir <- system.file("inst/extdata/solarAssoc/", package = "solarius")
genocov.files <- file.path(dir, "snp.genocov")
snplists.files <- file.path(dir, "snp.geno-list2")
snpmap.files <- file.path(dir, "map.snp.1")
snplists.length <- length(readLines(snplists.files))
mod <- solarAssoc(trait ~ 1, phenodata, genocov.files = genocov.files, snplists.files = snplists.files, snpmap.files = snpmap.files)
expect_true(nrow(mod$snpf) == snplists.length)
expect_true("pos" %in% colnames(mod$snpf))
expect_true(sum(is.na(mod$snpf$pos)) == 0)
})
test_that("`2 genocov.files` & 2 `snplists.files` & 2 `snpmap.files`", {
data(dat50)
dir <- system.file("inst/extdata/solarAssoc/", package = "solarius")
genocov.files <- file.path(dir, c("snp.genocov2", "snp.genocov3"))
snplists.files <- file.path(dir, c("snp.geno-list2", "snp.geno-list3"))
snpmap.files <- file.path(dir, c("map.snp.1.2", "map.snp.1.3"))
snplists.length <- sum(laply(snplists.files, function(x) length(readLines(x))))
mod <- solarAssoc(trait ~ 1, phenodata, genocov.files = genocov.files, snplists.files = snplists.files, snpmap.files = snpmap.files)
expect_true(nrow(mod$snpf) == snplists.length)
expect_true("pos" %in% colnames(mod$snpf))
expect_true(sum(is.na(mod$snpf$pos)) == 0)
})
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