context("LANL_HLA")
test_that("LANL_HLA_data Class Constructor works", {
x <- data.frame(dude = 'CAP117', mutation = 'B*3501')
expect_that(.LANL_HLA_data(x), throws_error("incorrent column names"))
x <- structure(list(epitope = c("MGARASVLSG", "ASVLSGGEL", "ASILRGGKLDK"),
gene_name = c("Gag_p17", "Gag_p17", "Gag_p17"),
start_pos = c(1L, 5L, 5L),
end_pos = c(10L, 13L, 15L),
subprotein = c("","",""),
hxb2_dna_position = c("", "", ""),
sub_type = c("CRF01_AE", "B", "C"),
organism = c("human", "human", "human"),
hla_genotype = c("", "", "")),
.Names = c("epitope", "gene_name", "start_pos", "end_pos", "subprotein",
"hxb2_dna_position", "sub_type", "organism", "hla_genotype"),
row.names = c(NA, 3L),
class = "data.frame")
expect_that(.LANL_HLA_data(x[0,]), throws_error("Must describe at least HLA genotype"))
expect_that(.LANL_HLA_data(x), is_a('LANL_HLA_data'))
})
test_that("read_patient_hla works", {
# x <- read_lanl_hla(file.path(find.package('EpitopeMatcher', .libPaths()),
# 'test_data/lanl_hla_test_file.csv'))
x <- get_test_lanl_hla_data()
expect_that(x, is_a('LANL_HLA_data'))
expect_that(digest(x), equals("c8ffd415e9e5d74f9e068a8907590d74"))
})
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