#library(FirebrowseR)
context("Analyses.CopyNumber.Genes.Deleted")
test_that("Getting the GISTIC2 delted ouput", {
format = "csv"
cohort = ""
gene = "PTEN"
q = 0.05
page = 1
page_size = 250
sort_by = "cohort"
obj = Analyses.CopyNumber.Genes.Deleted(format = format,
cohort = cohort,
gene = gene,
q = q,
page = page,
page_size = page_size,
sort_by = sort_by)
test.q = "http://firebrowse.org/api/v1/Analyses/CopyNumber/Genes/Deleted?format=csv&gene=PTEN&q=0.05&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 = "PFN3"
obj = Analyses.CopyNumber.Genes.Deleted(format = format,
cohort = cohort,
gene = gene,
q = q,
page = page,
page_size = page_size,
sort_by = sort_by)
test.q = "http://firebrowse.org/api/v1/Analyses/CopyNumber/Genes/Deleted?format=csv&gene=PFN3&q=0.05&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.Deleted(format = format,
cohort = cohort,
gene = gene,
q = q,
page = page,
page_size = page_size,
sort_by = sort_by)
expect_equal(length(obj[[1]]), nrow(test.obj))
expect_equal(length(obj[[1]][[1]]), ncol(test.obj))
})
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