Nothing
context("pqtl")
test_that("pqtl protein endpoint", {
skip_on_cran()
url <- getOption("epigraphdb.api.url")
query <- "ADAM19"
rtype <- "mrres"
pvalue <- 0.05
searchflag <- "proteins"
r <- httr::RETRY("GET", glue::glue("{url}/pqtl/"),
query = list(
query = query,
rtype = rtype,
pvalue = pvalue,
searchflag = searchflag
),
config = httr::add_headers(.headers = c("client-type" = "R", "ci" = "true"))
)
expect_equal(httr::status_code(r), 200)
expect_true(length(httr::content(r)) > 0)
})
test_that("pqtl trait endpoint", {
skip_on_cran()
url <- getOption("epigraphdb.api.url")
query <- "Inflammatory bowel disease"
rtype <- "mrres"
pvalue <- 0.05
searchflag <- "traits"
r <- httr::RETRY("GET", glue::glue("{url}/pqtl/"),
query = list(
query = query,
rtype = rtype,
pvalue = pvalue,
searchflag = searchflag
),
config = httr::add_headers(.headers = c("client-type" = "R", "ci" = "true"))
)
expect_equal(httr::status_code(r), 200)
})
test_that("pqtl_pleio endpoint", {
skip_on_cran()
url <- getOption("epigraphdb.api.url")
rsid <- "rs1260326"
prflag <- "proteins"
r <- httr::RETRY("GET", glue::glue("{url}/pqtl/pleio/"),
query = list(
rsid = rsid,
prflag = prflag
),
config = httr::add_headers(.headers = c("client-type" = "R", "ci" = "true"))
)
expect_equal(httr::status_code(r), 200)
})
test_that("pqtl_list endpoint", {
skip_on_cran()
url <- getOption("epigraphdb.api.url")
flag <- "exposures"
r <- httr::RETRY("GET", glue::glue("{url}/pqtl/list/"),
query = list(
flag = flag
),
config = httr::add_headers(.headers = c("client-type" = "R", "ci" = "true"))
)
expect_equal(httr::status_code(r), 200)
})
test_that("pqtl correct input", {
skip_on_cran()
query <- "Inflammatory bowel disease"
rtype <- "mrres"
pvalue <- 0.05
searchflag <- "traits"
r <- pqtl(
query = query,
rtype = rtype,
pvalue = pvalue,
searchflag = searchflag,
mode = "table"
)
expect_is(r, "tbl_df")
expect_true(dim(r)[1] > 0)
})
test_that("pqtl incorrect input", {
skip_on_cran()
query <- "Inflammatory bowel disease"
rtype <- "mrress"
pvalue <- 0.05
searchflag <- "traits"
expect_error(
r <- pqtl(
query = query,
rtype = rtype,
pvalue = pvalue,
searchflag = searchflag
)
)
})
test_that("pqtl not found input", {
skip_on_cran()
query <- "ADAM199999"
rtype <- "mrres"
pvalue <- 0.05
searchflag <- "proteins"
r <- pqtl(
query = query,
rtype = rtype,
pvalue = pvalue,
searchflag = searchflag
)
expect_equal(dim(r), c(0, 0))
})
test_that("pqtl_pleio correct input for a list of proteins", {
skip_on_cran()
rsid <- "rs1260326"
prflag <- "proteins"
r <- pqtl_pleio(
rsid = rsid,
prflag = prflag
)
expect_true(dim(r)[1] > 0)
})
test_that("pqtl_pleio correct input for a count", {
skip_on_cran()
rsid <- "rs1260326"
prflag <- "count"
r <- pqtl_pleio(
rsid = rsid,
prflag = prflag
)
expect_equal(r, 3)
})
test_that("pqtl_pleio incorrect input", {
skip_on_cran()
rsid <- "rs1260326"
prflag <- "countt"
expect_error(
r <- pqtl_pleio(
rsid = rsid,
prflag = prflag
)
)
})
test_that("pqtl_pleio not found input", {
skip_on_cran()
rsid <- "rs1260326gggg"
prflag <- "proteins"
r <- pqtl_pleio(
rsid = rsid,
prflag = prflag
)
expect_equal(dim(r), c(0, 0))
})
test_that("pqtl_list raw", {
skip_on_cran()
flag <- "exposures"
r <- pqtl_list(
flag = flag,
mode = "raw"
)
expect_true(length(r) > 1)
})
test_that("pqtl_list correct exposures input", {
skip_on_cran()
flag <- "exposures"
r <- pqtl_list(
flag = flag
)
expect_is(r, "tbl_df")
expect_true(dim(r)[1] > 0)
})
test_that("pqtl_list correct outcomes input", {
skip_on_cran()
flag <- "outcomes"
r <- pqtl_list(
flag = flag
)
expect_is(r, "tbl_df")
expect_true(dim(r)[1] > 0)
})
test_that("pqtl_list incorrect input", {
skip_on_cran()
flag <- "foobar"
expect_error(
r <- pqtl_list(
flag = flag
)
)
})
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