Nothing
# This extends tests in test-basic-workflow.R
# Skip these tests on CRAN
skip_on_cran()
xe <- XenaGenerate(subset = grepl("BRCA", XenaCohorts))
xe2 <- XenaHub(hostName = "tcgaHub")
xe3 <- XenaHub(
hosts = "https://tcga.xenahubs.net",
cohorts = "TCGA Breast Cancer (BRCA)",
datasets = "TCGA.BRCA.sampleMap/HiSeqV2"
)
all_hosts <- c(
"https://ucscpublic.xenahubs.net",
"https://tcga.xenahubs.net",
"https://gdc.xenahubs.net",
"https://icgc.xenahubs.net",
"https://toil.xenahubs.net",
"https://pancanatlas.xenahubs.net",
"https://xena.treehouse.gi.ucsc.edu:443",
"https://pcawg.xenahubs.net",
"https://atacseq.xenahubs.net",
"https://singlecellnew.xenahubs.net",
"https://kidsfirst.xenahubs.net"
#"https://tdi.xenahubs.net"
)
# XenaHub-class.R ---------------------------------------------------------
test_that("show method for XenaHub object works", {
expect_output(show(xe), "class: XenaHub")
})
test_that("fun xena_default_hosts works", {
expect_identical(xena_default_hosts(), all_hosts)
})
test_that("fun XenaHub works", {
expect_output(show(xe2), "class: XenaHub")
expect_error(XenaHub(hostName = "xxx"))
expect_output(show(xe3), "class: XenaHub")
})
test_that("fun .collapse_list works", {
expect_identical(.collapse_list(c("a", "b")), "a,b")
})
# api-higher --------------------------------------------------------------
test_that("funs to get hosts, cohorts, datasets and samples work", {
expect_identical("https://tcga.xenahubs.net", hosts(xe3))
expect_identical("TCGA Breast Cancer (BRCA)", cohorts(xe3))
expect_identical("TCGA.BRCA.sampleMap/HiSeqV2", datasets(xe3))
samples <- samples(xe3)[[1]]
expect_true("TCGA-GI-A2C8-01" %in% samples)
})
# Fetch -------------------------------------------------------------------
host <- "https://toil.xenahubs.net"
dataset <- "tcga_RSEM_gene_tpm"
samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
genes <- c("TP53", "RB1", "PIK3CA")
fetch()
# Fetch samples
fetch_dataset_samples(host, dataset, 2)
# Fetch identifiers
tryCatch({
fetch_dataset_identifiers(host, dataset)
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
# Fetch expression value by probes
tryCatch({
fetch_dense_values(host, dataset, probes, samples, check = FALSE)
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
tryCatch({
fetch_dense_values(host, dataset, probes, samples[1], check = TRUE)
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
tryCatch({
fetch_dense_values(host, dataset, probes[1], samples[1], check = TRUE)
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
tryCatch({
fetch_dense_values(host, dataset, probes[1], samples[1], check = TRUE)
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
tryCatch({
expect_error(fetch_dense_values(host, dataset, probes[1], 33, check = TRUE))
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
tryCatch({
fetch_dense_values(host, dataset, c(probes[1], "xxx"), c(samples[1], "xxx"), check = TRUE)
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
# The following two are two time consuming
# fetch_dense_values(host, dataset, probes[1], check = TRUE)
# fetch_dense_values(host, dataset, samples = samples[1], check = TRUE)
# Fetch expression value by gene symbol (if the dataset has probeMap)
tryCatch({
fetch_dense_values(host, dataset, genes, samples, check = TRUE, use_probeMap = TRUE)
}, error = function(e) {
if (grepl("500", e$message)) {
message("Bad network, skipping check")
} else {
stop(e$message)
}
})
# Workflow ----------------------------------------------------------------
expect_warning(XenaFilter(xe))
expect_warning(XenaFilter(xe2, filterCohorts = "TCGA Breast Cancer (BRCA)"))
XenaQueryProbeMap(xe3)
# clean all
rm(list = ls())
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.