test_that("expected datasts", {
# transpose to 1 col/dataframe
synapse_tables_wide <- genieBPC::synapse_tables %>%
dplyr::arrange(df) %>%
tidyr::pivot_wider(id_cols = c(cohort, version, release_date),
names_from = df,
values_from = synapse_id,
)
# expect only pre-specified names
expect_equal(names(synapse_tables_wide),
c("cohort", "version", "release_date",
"pt_char", "ca_dx_index", "ca_dx_non_index",
"ca_drugs", "prissmm_imaging", "prissmm_pathology",
"ca_radtx", "prissmm_md", "tumor_marker", "cpt",
"mutations_extended", "fusions", "cna",
"variable_synopsis"))
# expect all data releases to have the following data frames
expect_equal(nrow(synapse_tables_wide),
nrow(synapse_tables_wide %>%
tidyr::drop_na(pt_char, ca_dx_index, ca_dx_non_index,
ca_drugs, prissmm_imaging, prissmm_pathology,
prissmm_md, cpt,
mutations_extended, fusions, cna,
variable_synopsis)))
# expect only certain cohorts to have tumor marker data
synapse_tables_wide_tm_cohorts <- synapse_tables_wide %>%
dplyr::filter(stringr::str_to_upper(cohort) %in% c("CRC", "BRCA", "PANC", "PROSTATE"))
expect_equal(nrow(synapse_tables_wide_tm_cohorts),
nrow(synapse_tables_wide %>%
tidyr::drop_na(tumor_marker)))
# expect onlycertain cohorts to have radiation data
synapse_tables_wide_rt_cohorts <- synapse_tables_wide %>%
dplyr::filter(stringr::str_to_upper(cohort) %in% c("PANC", "PROSTATE", "BLADDER"))
expect_equal(nrow(synapse_tables_wide_rt_cohorts),
nrow(synapse_tables_wide %>%
tidyr:: drop_na(ca_radtx)))
# cohort, version and release dates always populated"
expect_equal(nrow(synapse_tables_wide),
nrow(synapse_tables_wide %>%
tidyr::drop_na(cohort, version, release_date)))
})
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