#' Copyright(c) 2017-2020 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("getGenotypes")
## This is identical to getPedigree and needs to be strengthened. However,
## function does not do any data quality checks at this time.
test_that("getGenotypes recognizes no file and wrong file arguments", {
expect_error(getGenotypes(), "\"fileName\" is missing, with no default")
})
test_that("getGenotypes recognizes and opens Excel files.", {
pedExcel <-
suppressWarnings(getGenotypes(
fileName = system.file("testdata", "qcPed.xlsx",
package =
"nprcgenekeepr")
))
expect_equal(nrow(pedExcel), 280)
})
test_that(
paste0(
"getGenotypes recognizes and opens CSV files with default ",
"comma separator."
),
{
pedCsv <-
getGenotypes(fileName = system.file("testdata", "qcPed.csv",
package =
"nprcgenekeepr"))
expect_equal(nrow(pedCsv), 280)
}
)
test_that(
paste0(
"getGenotypes recognizes and opens CSV files with specified ",
"comma separator."
),
{
pedCsv2 <-
getGenotypes(
fileName = system.file("testdata", "qcPed.csv",
package =
"nprcgenekeepr"),
sep = ","
)
expect_equal(nrow(pedCsv2), 280)
}
)
test_that(
paste0(
"getGenotypes recognizes and opens .txt files with specified ",
"tab separator."
),
{
pedTxt <-
getGenotypes(
fileName = system.file("testdata", "qcPed.txt",
package =
"nprcgenekeepr"),
sep = "\t"
)
expect_equal(nrow(pedTxt), 280)
}
)
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