tests/testthat/test_return_colnames.R

In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

test_that("return gnomad_genome colnames", {
  database.dir <- system.file("extdata", "demo", package = "anor")
  chr <- c("chr1", "chr2", "chr1")
  start <- c("10020", "10020", "10020")
  end <- c("10020", "10020", "10020")
  ref <- c("A", "A", "A")
  alt <- c("-", "-", "-")
  dat <- data.table(chr = chr, start = start, end = end, ref = ref, alt = alt)
  x <- annotation(dat, "gnomad_exome", database.dir = database.dir, db.type = "txt")
  expect_equal(is.na(x[1, gnomAD_exome_ALL]), TRUE)
  expect_equal(length(colnames(x)), 9)
  expect_equal(colnames(x)[1], "gnomAD_exome_ALL")
  expect_equal(colnames(x)[9], "gnomAD_exome_SAS")
  chr <- c("chr1", "chr2", "chr1")
  start <- c("12198", "10020", "10020")
  end <- c("12198", "10020", "10020")
  ref <- c("G", "A", "A")
  alt <- c("C", "-", "-")
  dat <- data.table(chr = chr, start = start, end = end, ref = ref, alt = alt)
  x <- annotation(dat, "gnomad_exome", database.dir = database.dir, db.type = "txt")
  expect_equal(length(colnames(x)), 9)
  expect_equal(colnames(x)[1], "gnomAD_exome_ALL")
  expect_equal(colnames(x)[9], "gnomAD_exome_SAS")
  expect_equal(x[1, gnomAD_exome_ALL], ".")
})