Nothing
test_that("missing directory", {
expect_error(load_rcc(
# data_directory = "salmon_data",
ssheet_csv = salmon_tidy,
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = FALSE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
))
})
test_that("missing sample sheet", {
expect_error(load_rcc(
data_directory = "salmon_data",
# ssheet_csv = salmon_tidy,
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = FALSE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
))
})
test_that("missing id_colname", {
expect_error(load_rcc(
data_directory = "salmon_data",
ssheet_csv = salmon_tidy,
# id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = FALSE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
))
})
test_that("no housekeeping norm", {
expect_s3_class({
load_rcc(
data_directory = "salmon_data",
ssheet_csv = salmon_tidy,
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = FALSE,
housekeeping_norm = FALSE,
normalisation_method = "GLM",
n_comp = 10
)
}, "nacho")
})
test_that("no housekeeping norm and prediction", {
expect_s3_class({
load_rcc(
data_directory = "salmon_data",
ssheet_csv = salmon_tidy,
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = TRUE,
housekeeping_norm = FALSE,
normalisation_method = "GLM",
n_comp = 10
)
}, "nacho")
})
test_that("using GEO", {
gse <- try(GEOquery::getGEO(GEO = "GSE74821"), silent = TRUE)
if (!inherits(gse, "try-error")) {
targets <- Biobase::pData(Biobase::phenoData(gse[[1]]))
geo_files <- try(GEOquery::getGEOSuppFiles(GEO = "GSE74821", baseDir = tempdir()), silent = TRUE)
if (!inherits(geo_files, "try-error")) {
utils::untar(file.path(tempdir(), "GSE74821", "GSE74821_RAW.tar"), exdir = file.path(tempdir(), "GSE74821"))
targets$IDFILE <- list.files(path = file.path(tempdir(), "GSE74821"), pattern = ".RCC.gz$")
targets[] <- lapply(X = targets, FUN = iconv, from = "latin1", to = "ASCII")
# test_that("using GEO GSE74821", {
expect_s3_class({
load_rcc(
data_directory = file.path(tempdir(), "GSE74821"),
ssheet_csv = head(targets, 20),
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = FALSE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
)
}, "nacho")
# })
# test_that("using GEO GSE74821 with prediction", {
expect_s3_class({
load_rcc(
data_directory = file.path(tempdir(), "GSE74821"),
ssheet_csv = head(targets, 20),
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = TRUE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
)
}, "nacho")
# })
}
}
closeAllConnections()
gse <- try(GEOquery::getGEO(GEO = "GSE70970"), silent = TRUE)
if (!inherits(gse, "try-error")) {
targets <- Biobase::pData(Biobase::phenoData(gse[[1]]))
geo_files <- try(GEOquery::getGEOSuppFiles(GEO = "GSE70970", baseDir = tempdir()), silent = TRUE)
if (!inherits(geo_files, "try-error")) {
utils::untar(file.path(tempdir(), "GSE70970", "GSE70970_RAW.tar"), exdir = file.path(tempdir(), "GSE70970"))
targets$IDFILE <- list.files(path = file.path(tempdir(), "GSE70970"), pattern = ".RCC.gz$")
targets[] <- lapply(X = targets, FUN = iconv, from = "latin1", to = "ASCII")
# test_that("using GEO GSE70970", {
expect_s3_class({
load_rcc(
data_directory = file.path(tempdir(), "GSE70970"),
ssheet_csv = head(targets, 20),
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = FALSE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
)
}, "nacho")
# })
# test_that("using GEO GSE70970 with prediction", {
expect_s3_class({
load_rcc(
data_directory = file.path(tempdir(), "GSE70970"),
ssheet_csv = head(targets, 20),
id_colname = "IDFILE",
housekeeping_genes = NULL,
housekeeping_predict = TRUE,
housekeeping_norm = TRUE,
normalisation_method = "GLM",
n_comp = 10
)
}, "nacho")
# })
# test_that("ssheet_csv as vector", {
expect_s3_class({
load_rcc(
data_directory = file.path(tempdir(), "GSE70970"),
ssheet_csv = head(targets[["IDFILE"]], 20),
id_colname = "IDFILE",
housekeeping_predict = TRUE,
housekeeping_norm = TRUE
)
},
class = "nacho"
)
# })
# test_that("ssheet_csv as vector without id_colname", {
expect_s3_class({
load_rcc(
data_directory = file.path(tempdir(), "GSE70970"),
ssheet_csv = head(targets[["IDFILE"]], 20),
housekeeping_predict = TRUE,
housekeeping_norm = TRUE
)
},
class = "nacho"
)
# })
# test_that("ssheet_csv as a named vector", {
expect_s3_class({
load_rcc(
data_directory = file.path(tempdir(), "GSE70970"),
ssheet_csv = `names<-`(
head(targets[["IDFILE"]], 20),
head(letters, 20)
),
# id_colname = "IDFILE",
housekeeping_predict = TRUE,
housekeeping_norm = TRUE
)
},
class = "nacho"
)
# })
# test_that("id_colname not defined when using df", {
expect_error({
load_rcc(
data_directory = file.path(tempdir(), "GSE70970"),
ssheet_csv = head(targets, 20),
housekeeping_predict = TRUE,
housekeeping_norm = TRUE
)
})
# })
}
}
closeAllConnections()
# test_that("using RAW RCC multiplexed", {
expect_s3_class({
load_rcc(
data_directory = "salmon_data",
ssheet_csv = salmon_tidy,
id_colname = "IDFILE"
)
}, "nacho")
# })
# test_that("using RAW RCC multiplexed without plexset_id", {
targets_tidy <- salmon_tidy
targets_tidy$plexset_id <- NULL
expect_error({
load_rcc(
data_directory = "salmon_data",
ssheet_csv = targets_tidy,
id_colname = "IDFILE"
)
})
# })
# test_that("using RAW RCC multiplexed with wrong path", {
targets_tidy <- salmon_tidy
targets_tidy$IDFILE[1] <- "something_wrong.RCC" # wrong path
expect_error({
load_rcc(
data_directory = "salmon_data",
ssheet_csv = targets_tidy,
id_colname = "IDFILE"
)
})
# })
# test_that("Too high number of components", {
expect_message({
load_rcc(
data_directory = "salmon_data",
ssheet_csv = salmon_tidy,
id_colname = "IDFILE",
n_comp = 1000
)
}, "has been set to")
# })
# test_that("plexset", {
expect_s3_class({
load_rcc(
data_directory = "plexset_data",
ssheet_csv = plexset_tidy,
id_colname = "IDFILE",
housekeeping_predict = TRUE,
housekeeping_norm = TRUE
)
},
class = "nacho"
)
# })
# test_that("heterogenous", {
expect_error({
load_rcc(
data_directory = ".",
ssheet_csv = plexset_salmon_tidy,
id_colname = "IDFILE",
housekeeping_predict = TRUE,
housekeeping_norm = TRUE
)
}
)
# })
})
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