Nothing
# This code tests the retrieveMatrix function
# library(magmaR); library(testthat); source("tests/testthat/helper-magmaR.R"); source("tests/testthat/test-matrix.R")
targ <- magmaRset(
token = TOKEN,
url = URL)
vcr::use_cassette("matrix", {
ids <- retrieveIds(targ, "example", "rna_seq")
test_that("retrieveMatrix", {
mat <- retrieveMatrix(
targ,
"example",
"rna_seq",
attributeNames = "gene_counts")
expect_type(mat, "integer")
expect_equal(dim(mat), c(40,12))
# Column names = identifiers
expect_true(all(colnames(mat) %in% ids))
# Row names = gene names (pulled from template)
expect_equivalent(rownames(mat), paste0("gene", 1:40))
})
test_that("retrieveMatrix warns but ignores empty records", {
expect_warning(
mat <- retrieveMatrix(
targ,
"example",
"rna_seq",
recordNames = c(ids, "not_a_record"),
attributeNames = "gene_counts"),
"Empty record, not_a_record, was ignored."
)
expect_type(mat, "integer")
expect_equal(dim(mat), c(40,12))
})
})
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