tests/testthat/test.Analyses.Mutation.MAF.R

In mariodeng/FirebrowseR: An 'API' Client for Broads 'Firehose' Pipeline

#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)

})