testsOld/testthat/test_04addrse.R

In isglobal-brge/MultiDataSet: Implementation of MultiDataSet and ResultSet

# context("add SE and RSE")
# library(GenomicRanges)
# library(SummarizedExperiment)
# 
# 
# # SummarizedExperiment ####
# test_that("add SummarizedExperiment", {
#     multi <- createMultiDataSet()
#     
#     nrows <- 10; ncols <- 6
#     counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
#     colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
#                          row.names=LETTERS[1:6])
#     rowData <- DataFrame(chr = "chr1", start = 1:10, end = 11:20)
#     se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
#                                 colData=colData, rowData = rowData)
#     
#     expect_s4_class(multi2 <- add_se(multi, se0, "seEx"), "MultiDataSet")
#     expect_equal(names(multi2), "seEx")
#     expect_s4_class(multi2[["seEx"]], "SummarizedExperiment")
#     
#     
#     # Check Overwrite ####
#     expect_error(add_se(multi2, se0, "seEx"), "There is already an object in this slot. Set overwrite = TRUE to overwrite the previous set.")
#     expect_warning(add_se(multi2, se0, "seEx", overwrite = TRUE), "Slot 'seEx' is already set in 'MultiDataSet'. Previous content will be overwritten.")
#     
#     # Check GRanges
#     gr <- makeGRangesFromDataFrame(rowData)
#     expect_s4_class(multi2 <- add_se(multi, se0, "seEx", GRanges = gr), "MultiDataSet")
#     
#     expect_s4_class(multi2 <- add_se(multi, se0, "seEx", GRanges = NA), "MultiDataSet")
#     
#     expect_error(multi2 <- add_se(multi, se0, "seEx", GRanges = "cot"), "GRanges should be a GenomicRanges or NA.")
# })
# 
# 
# # RangedSummarizedExperiment ####
# test_that("add RangedSummarizedExperiment", {
#   multi <- createMultiDataSet()
#   
#   counts <- matrix(runif(200 * 6, 1, 1e4), 200)
#   rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
#                        IRanges(floor(runif(200, 1e5, 1e6)), width=100),
#                        strand=sample(c("+", "-"), 200, TRUE),
#                        feature_id=sprintf("ID%03d", 1:200))
#   colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
#                        row.names=LETTERS[1:6], id = LETTERS[1:6])
#   names(rowRanges) <- 1:200
#   rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
#                               rowRanges=rowRanges, colData=colData)
#   
#   multi <- add_rse(multi, rse, "rseEx")
#   expect_equal(names(multi), "rseEx")
#   
#   expect_error(add_rse(multi, rse, "rseEx"), "There is already an object in this slot. Set overwrite = TRUE to overwrite the previous set.")
#   expect_warning(add_rse(multi, rse, "rseEx", overwrite = TRUE), "Slot 'rseEx' is already set in 'MultiDataSet'. Previous content will be overwritten.")
#   
#   
#   
#   expect_s4_class(multi[["rseEx"]], "RangedSummarizedExperiment")
# 
#   library(minfiData)
#   data("MsetEx")
#   GRset <- mapToGenome(MsetEx[1:10, 1:2])
#   
#   expect_warning(multi2 <- add_rse(multi, GRset, "GRSet"), "No id column found in colData. The id will be equal to the sampleNames")
#   expect_equal(sampleNames(multi2[["GRSet"]]), c("5723646052_R02C02", "5723646052_R04C01"))
#   expect_equal(multi2[["GRSet"]]$id, c("5723646052_R02C02", "5723646052_R04C01"))
#   
#   colData(GRset)$id <- letters[1:2]
#   multi2 <- add_rse(multi, GRset, "GRSet")
#   expect_is(multi2[["GRSet"]], "GenomicMethylSet")
#   expect_equal(sampleNames(multi2[["GRSet"]]), c("5723646052_R02C02", "5723646052_R04C01"))
#   expect_equal(multi2[["GRSet"]]$id, c("a", "b"))
# })