Nothing
context("HGVSnames")
test_that("Substitution works", {
output <- HGVSnames(start = 45576, ref = "A", alt = "C")
expect_equal(output, "g.45576A>C")
output <- HGVSnames(start = "88+1", ref = "G", alt = "T", type = "c")
expect_equal(output, "c.88+1G>T")
})
test_that("Deletion / insertion (indel) works", {
output <- HGVSnames(start = 6775, ref = "T", alt = "GA")
expect_equal(output, "g.6775delinsGA")
output <- HGVSnames(start = 6775, ref = "TCA", alt = "C")
expect_equal(output, "g.6775_6777delinsC")
output <- HGVSnames(start = 145, ref = "CGA", alt = "TGG", type = "c")
expect_equal(output, "c.145_147delinsTGG")
output <- HGVSnames(start = 9002, ref = "AAAAAAAA", alt = "TTT")
expect_equal(output, "g.9002_9009delinsTTT")
output <- HGVSnames(start = 4, ref = "GC", alt = "TG")
expect_equal(output, "g.4_5delinsTG")
})
test_that("seqnames parameter works", {
output <- HGVSnames(start = 12345611, ref = "G", alt = "A", seqnames = "chr11")
expect_equal(output, "chr11:g.12345611G>A")
})
test_that("Vectorization works", {
start <- c(45576, "88+1", 6775, 6775, 145, 9002, 4, 12345611)
ref <- c("A", "G", "T", "TCA", "CGA", "AAAAAAAA", "GC", "G")
alt <- c("C", "T", "GA", "C", "TGG", "TTT", "TG", "A")
type <- c("g", "c", "g", "g", "c", "g", "g", "g")
seqnames <- c("", "", NA, NA, NA, NA, NA, "chr11")
output <- HGVSnames(start, ref, alt, type, seqnames)
expect_equal(output, c("g.45576A>C", "c.88+1G>T", "g.6775delinsGA",
"g.6775_6777delinsC", "c.145_147delinsTGG", "g.9002_9009delinsTTT",
"g.4_5delinsTG", "chr11:g.12345611G>A"))
})
test_that("alt paramter with * works", {
output <- HGVSnames(start = 58347698, ref = "A", alt = "*")
expect_equal(output, "g.58347698del")
})
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