test_that("eQTLcatalogue_query works", {
library(dplyr)
sumstats_paths <- echodata::get_Nalls2019_loci(limit_snps = 5)[seq_len(2)]
qtl_search <- c("Alasoo_2018.macrophage_naive")
#### Method 1: Merged results ####
GWAS.QTL <- catalogueR::eQTLcatalogue_query(
sumstats_paths = sumstats_paths,
qtl_search = qtl_search,
merge_with_gwas = TRUE,
split_files = FALSE
)
testthat::expect_true(methods::is(GWAS.QTL, "data.table"))
testthat::expect_equal(dim(GWAS.QTL),c(80,56))
testthat::expect_true(all(qtl_search %in% unique(GWAS.QTL$qtl_id)))
#### Method 2: Split results ####
gwas.qtl_paths <- catalogueR::eQTLcatalogue_query(
sumstats_paths = sumstats_paths,
qtl_search = qtl_search,
merge_with_gwas = TRUE,
split_files = TRUE
)
for (f in names(gwas.qtl_paths)) {
print(f)
dat <- data.table::fread(gwas.qtl_paths[[f]])
testthat::expect_equal(dim(dat),c(55,53))
}
#### Gather files ####
GWAS.QTL2 <- catalogueR::merge_files(file_paths = gwas.qtl_paths)
testthat::expect_true(methods::is(GWAS.QTL2, "data.table"))
testthat::expect_equal(nrow(GWAS.QTL), nrow(GWAS.QTL2))
})
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