test_that("eQTLcatalogue_fetch works", {
data("meta")
unique_id <- meta$unique_id[1]
paths <- echodata::get_Nalls2019_loci(limit_snps = 5)
query_dat <- data.table::fread(paths$BST1)
#### Using data ####
gwas.qtl <- catalogueR::eQTLcatalogue_fetch(
unique_id = unique_id,
query_granges = query_dat,
method = "REST"
)
testthat::expect_true(methods::is(gwas.qtl, "data.table"))
testthat::expect_gte(nrow(gwas.qtl), 1200)
#### using explicit range ####
query_granges <- echotabix::construct_query(
query_chrom = query_dat$CHR[[1]],
query_start_pos = min(query_dat$POS),
query_end_pos = max(query_dat$POS))
GWAS.QTL_manual <- catalogueR::eQTLcatalogue_fetch(
unique_id = unique_id,
query_granges = query_granges)
testthat::expect_true(methods::is(GWAS.QTL_manual, "data.table"))
testthat::expect_gte(nrow(GWAS.QTL_manual), 1200)
#### Compare across methods ####
testthat::expect_true(all.equal(gwas.qtl,
GWAS.QTL_manual))
#### Using tabix ####
## WARNING: if you test this iteratively, will eventually get blocked
## by the EMBL-EBI server.
gwas.qtl <- catalogueR::eQTLcatalogue_fetch(
unique_id = unique_id,
query_granges = query_dat,
method = "tabix"
)
testthat::expect_true(methods::is(gwas.qtl, "data.table"))
testthat::expect_gte(nrow(gwas.qtl), 1200)
})
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