context("object")
# connect to the db file
fl <- system.file('extdata', 'cRegulome.db', package = 'cRegulome')
conn <- RSQLite::dbConnect(RSQLite::SQLite(), fl)
test_that('objects cmicroRNA are constructed properly', {
dat <- get_mir(conn,
mir = 'hsa-let-7g',
study = 'STES',
min_abs_cor = .3,
max_num = 5)
cmir <- cmicroRNA(dat)
expect_s3_class(cmir, 'cmicroRNA')
expect_identical(names(cmir), c("microRNA", "features", "studies", "corr"))
expect_identical(cmir$microRNA, 'hsa-let-7g')
expect_identical(cmir$studies, 'STES')
expect_equal(length(cmir$features), 5)
expect_true(min(abs(cmir$corr[[1]][ ,1])) > .3)
})
test_that('objects cmicroRNA are constructed from multiple queries and filters', {
dat <- get_mir(conn,
mir = c('hsa-let-7g', 'hsa-mir-149'),
study = 'STES',
max_num = 5)
cmir <- cmicroRNA(dat)
expect_s3_class(cmir, 'cmicroRNA')
expect_identical(names(cmir), c("microRNA", "features", "studies", "corr"))
expect_identical(cmir$microRNA, c('hsa-let-7g', 'hsa-mir-149'))
expect_identical(cmir$studies, 'STES')
expect_true(nrow(cmir$corr[[1]]) >= 5)
})
test_that('objects cTF are constructed properly', {
dat <- get_tf(conn,
tf = 'LEF1',
study = 'STES',
min_abs_cor = .3,
max_num = 5)
ctf <- cTF(dat)
expect_s3_class(ctf, 'cTF')
expect_identical(names(ctf), c("TF", "features", "studies", "corr"))
expect_identical(ctf$TF, 'LEF1')
expect_identical(ctf$studies, 'STES')
expect_equal(length(ctf$features), 5)
expect_true(min(abs(ctf$corr[[1]][, 1])) > .3)
})
test_that('cTF works with more than two tfs', {
tf = c("TFAP2A", "ETV4", "LEF1", "MYB", "MYBL2")
dat <- get_tf(conn,
tf = tf,
study = 'STES')
ctf <- cTF(dat)
expect_equal(class(ctf), 'cTF')
expect_true(all(colnames(ctf$corr[[1]]) %in% tf))
})
# clean up
RSQLite::dbDisconnect(conn)
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