#library(FirebrowseR)
context("Analyses.CopyNumber.Genes.All")
test_that("Getting the GISTIC2 ouput", {
format = "csv"
cohort = "PRAD"
gene = "PTEN"
tcga_participant_barcode = c("TCGA-J4-A67O", "TCGA-G9-6496")
page = 1
page_size = 250
sort_by = "cohort"
obj = Analyses.CopyNumber.Genes.All(format = format,
cohort = cohort,
gene = gene,
tcga_participant_barcode = tcga_participant_barcode,
page = page,
page_size = page_size,
sort_by = sort_by)
test.q = "http://firebrowse.org/api/v1/Analyses/CopyNumber/Genes/All?format=csv&cohort=PRAD&gene=PTEN&tcga_participant_barcode=TCGA-J4-A67O%2CTCGA-G9-6496&page=1&page_size=250&sort_by=cohort"
test.obj = read.table(test.q, header = T, sep = ",")
expect_equal(nrow(obj), nrow(test.obj))
expect_equal(ncol(obj), ncol(test.obj))
gene = ""
obj = Analyses.CopyNumber.Genes.All(format = format,
cohort = cohort,
gene = gene,
tcga_participant_barcode = tcga_participant_barcode,
page = page,
page_size = page_size,
sort_by = sort_by)
test.q = "http://firebrowse.org/api/v1/Analyses/CopyNumber/Genes/All?format=csv&cohort=PRAD&tcga_participant_barcode=TCGA-J4-A67O%2CTCGA-G9-6496&page=1&page_size=250&sort_by=cohort"
test.obj = read.table(test.q, header = T, sep = ",")
expect_equal(nrow(obj), nrow(test.obj))
expect_equal(ncol(obj), ncol(test.obj))
format = "json"
obj = Analyses.CopyNumber.Genes.All(format = format,
cohort = cohort,
gene = gene,
tcga_participant_barcode = tcga_participant_barcode,
page = page,
page_size = page_size,
sort_by = sort_by)
expect_equal(length(obj[[1]]), nrow(test.obj))
})
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