Nothing
context('methods.tidy')
# connect to the db file
fl <- system.file('extdata', 'cRegulome.db', package = 'cRegulome')
conn <- RSQLite::dbConnect(RSQLite::SQLite(), fl)
test_that('cor_tidy output a data.frame identical to output of get_mir', {
dat <- get_mir(conn,
mir = 'hsa-let-7g',
study = 'STES',
min_abs_cor = .3,
max_num = 5)
cmir <- cmicroRNA(dat)
tidy_cmir <- cor_tidy(cmir)
expect_equal(dat, tidy_cmir)
})
test_that('cor_tidy works with mulitple queries', {
dat <- get_mir(conn,
mir = c('hsa-let-7g', 'hsa-mir-149'),
study = 'STES',
max_num = 5)
cmir <- cmicroRNA(dat)
tidy_cmir <- cor_tidy(cmir)
expect_true(all(dat$mirna_base %in% tidy_cmir$mirna_base))
expect_true(all(dat$feature %in% tidy_cmir$feature))
})
test_that('tidy output a data.frame identical to output of get_tf', {
dat <- get_tf(conn,
tf = 'LEF1',
study = 'STES',
min_abs_cor = .3,
max_num = 5)
ctf <- cTF(dat)
tidy_tf <- cor_tidy(ctf)
expect_equal(dat, tidy_tf)
})
test_that("cor_igraph retruns a the proper object", {
dat <- get_mir(conn,
mir = 'hsa-let-7g',
study = 'STES',
min_abs_cor = .3,
max_num = 5)
cmir <- cmicroRNA(dat)
g <- cor_igraph(cmir)
expect_s3_class(g, 'igraph')
dat <- get_tf(conn,
tf = 'LEF1',
study = 'STES',
min_abs_cor = .3,
max_num = 5)
ctf <- cTF(dat)
g <- cor_igraph(ctf)
expect_s3_class(g, 'igraph')
})
test_that('cor_prep works', {
dat <- get_tf(conn,
tf = 'LEF1',
study = 'STES',
min_abs_cor = .3,
max_num = 5)
ctf <- cTF(dat)
df <- cor_prep(ctf, 'STES')
expect_true(is.data.frame(df))
expect_true('Direction' %in% names(df))
expect_true('Correlation' %in% names(df))
expect_equal(unique(df$study), 'STES')
})
test_that('cor_prep works with multiple queries', {
dat <- get_mir(conn,
mir = c('hsa-let-7g', 'hsa-let-7i'),
study = 'STES')
cmir <- cmicroRNA(dat)
df <- cor_prep(cmir, 'STES')
expect_true(is.data.frame(df))
expect_true('Direction' %in% names(df))
expect_true('Correlation' %in% names(df))
expect_equal(unique(df$study), "STES")
})
# clean up
RSQLite::dbDisconnect(conn)
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