context("Column label variants")
test_that("canonical labels recognized", {
file <- "tables/columns-variant1-canonical.txt"
labels <- names(.gwas_patterns)
expect_silent(table <- read_gwas(file, verbose = FALSE))
expect_equal(colnames(table), labels)
expect_equal(dim(table), c(5, 11))
})
test_that("abbreviated labels recognized", {
file <- "tables/columns-variant2-abbreviated.txt"
labels <- names(.gwas_patterns)
expect_silent(table <- read_gwas(file, verbose = FALSE))
expect_equal(colnames(table), labels)
expect_equal(dim(table), c(5, 11))
})
test_that("variant 3 recognized", {
file <- "tables/columns-variant3.txt"
labels <-
c("marker",
"position",
"a1",
"a2",
"frequency",
"pvalue")
expect_silent(table <- read_gwas(file, verbose = FALSE))
expect_equal(colnames(table), labels)
expect_equal(dim(table), c(5, 6))
})
test_that("variant 4", {
file <- "tables/columns-variant4.txt"
labels <-
c("marker",
"a1",
"a2",
"frequency",
"information",
"beta",
"se",
"pvalue")
expect_silent(table <- read_gwas(file, verbose = FALSE))
expect_equal(colnames(table), labels)
expect_equal(dim(table), c(9, 8))
})
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