#library(FirebrowseR)
context("Analyses.Mutation.MAF")
test_that("Getting MAF files", {
format = "json"
cohort = ""
tool = "MutSig2CV"
gene = ""
tcga_participant_barcode = ""
column = ""
page = 1
page_size = 250
sort_by = c("gene")
skip("To big to run")
expect_error(Analyses.Mutation.MAF(format = format,
cohort = cohort,
tool = tool,
gene =gene,
tcga_participant_barcode = tcga_participant_barcode,
column = column,
page = page,
page_size = page_size,
sort_by = sort_by))
gene = c("TP53", "RUNX1")
cohort = "COAD"
obj = Analyses.Mutation.MAF(format = format,
cohort = cohort,
tool = tool,
gene = gene,
tcga_participant_barcode = tcga_participant_barcode,
column = column,
page = page,
page_size = page_size,
sort_by = sort_by)
expect_is(obj, "list")
expect_that(length(obj[[1]]), equals(page_size))
tcga_participant_barcode = "TCGA-CH-5761"
cohort = "PRAD"
expect_error(Analyses.Mutation.MAF(format = format,
cohort = cohort,
tool = tool,
gene =gene,
tcga_participant_barcode = tcga_participant_barcode,
column = column,
page = page,
page_size = page_size,
sort_by = sort_by))
gene = ""
obj = Analyses.Mutation.MAF(format = format,
cohort = cohort,
tool = tool,
gene = gene,
tcga_participant_barcode = tcga_participant_barcode,
column = column,
page = page,
page_size = page_size,
sort_by = sort_by)
test.q = "http://firebrowse.org/api/v1/Analyses/Mutation/MAF?format=csv&cohort=PRAD&tool=MutSig2CV&tcga_participant_barcode=TCGA-CH-5761&page=1&page_size=250&sort_by=gene"
test.obj = read.table(test.q, header = T, sep = ",")
expect_equal(length(obj[[1]]), nrow(test.obj))
expect_equal(length(obj[[1]][[1]]), ncol(test.obj))
column = c("tcga_participant_barcode", "Hugo_Symbol", "Variant_Type")
obj = Analyses.Mutation.MAF(format = format,
cohort = cohort,
tool = tool,
gene = gene,
tcga_participant_barcode = tcga_participant_barcode,
column = column,
page = page,
page_size = page_size,
sort_by = sort_by)
expect_equal(length(obj[[1]][[1]]), 3)
})
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