Restore tests, start CI

.travis.yml

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+language: r
+
+sudo: required
+
+warnings_are_errors: true
+
+bioc_required: true
+
+r_github_packages:
+  - jimhester/covr
+
+after_success:
+- Rscript -e 'covr::codecov()'

tests/testthat.R

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+library(testthat)
+library(SomaticSignatures)
+
+test_check("SomaticSignatures")

tests/testthat/test-SomaticSignatures.R

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+library(testthat)
+library(SomaticSignatures)
+
+context("mutect")
+
+test_that("'readMutect' works", {
+    mutect_path = system.file("examples", "mutect.tsv", package = "variants")
+
+    expect_true( file.exists(mutect_path) )
+
+    vr1 = readMutect(mutect_path)
+    vr2 = readMutect(mutect_path, strip = TRUE)
+
+    expect_is( class(vr1), "VRanges" )
+    expect_is( class(vr2), "VRanges" )
+    expect_is( mcols(vr2), NULL )
+})
+
+
+context("granges-utils")
+
+mutect_path = system.file("examples", "mutect.tsv", package = "variants")
+vr2 = readMutect(mutect_path, strip = TRUE)
+
+test_that("'granges' works", {
+    gr2 = granges(vr2)
+
+    expect_is( class(gr2), "GRanges" )
+    expect_is( mcols(gr2), NULL)
+})
+
+test_that("'ucsc/ncbi' works", {
+    gr2 = granges(vr2)
+    gr2_ncbi = ncbi(gr2)
+    gr2_ucsc = ucsc(gr2_ncbi)
+
+    expect_identical(seqchar(gr2), seqchar(gr2_ucsc))
+})
+
+
+context("mutationContextMutect")
+
+test_that("'mutationContextMutect' works", {
+
+    mutect_path = system.file("examples", "mutect.tsv", package = "SomaticSignatures")
+    vr1 = readMutect(mutect_path)
+
+    ct1 = mutationContextMutect(vr1)
+    ct2 = mutationContextMutect(vr1, "normal_best_gt")
+
+    expect_is( class(ct1), "data.frame" )
+    expect_is( class(ct2), "data.frame" )
+
+    expect_error(mutationContextMutect(vr1, "notthere"))
+
+})
+
+
+context("mutationContext")
+
+test_that("'mutationContext' works", {
+
+    if(require(BSgenome.Hsapiens.1000genomes.hs37d5)) {
+
+        mutect_path = system.file("examples", "mutect.tsv", package = "SomaticSignatures")
+        vr0 = readMutect(mutect_path)
+        vr1 = vr0
+        mcols(vr1) = NULL
+
+        vr2 = mutationContextMutect(vr0)
+        vr1 = mutationContext(vr1, BSgenome.Hsapiens.1000genomes.hs37d5)
+        expect_equal(as.character(vr1$alteration), as.character(vr2$alteration))
+        expect_equal(as.character(vr1$context), as.character(vr2$context.1))
+
+        vr9 = vr1[1]
+        alt(vr9) = "CA"
+        expect_error(mutationContext(vr9, BSgenome.Hsapiens.1000genomes.hs37d5))
+
+        vr9 = vr1[1]
+        ref(vr9) = "CAT"
+        expect_error(mutationContext(vr9, BSgenome.Hsapiens.1000genomes.hs37d5))
+
+})
+
+
+context("datasets")
+
+test_that("datasets for processing are available", {
+
+    data("sca_mm", package = "SomaticSignatures")
+    expect_is( sca_mm, "matrix" )
+    expect_equal( nrow(sca_mm), 96 i)
+
+    data("sca_sigs", package = "SomaticSignatures")
+    expect_is( sigs_nmf, "MutationalSignatures" )
+    expect_is( sigs_pca, "MutationalSignatures" )    
+
+})
+
+context("identifySignatures")
+
+test_that("'identifySignatures' works", {
+
+    data("sca_mm", package = "SomaticSignatures")
+
+    sigs_nmf = identifySignatures(sca_mm, 3)
+    expect_is( sigs_nmf, "MutationalSignatures" )
+
+    ## as many signatures as samples
+    sigs_nmf = identifySignatures(sca_mm, ncol(sca_mm))
+    expect_is( sigs_nmf, "MutationalSignatures" )
+})
+
+
+test_that("'identifySignatures' handles bad inputs", {
+
+    data("sca_mm", package = "SomaticSignatures")
+
+    ## bad number of signatures
+    expect_error( identifySignatures(sca_mm, 0),
+                 ".*single, positive integer.*")
+
+    ## 'decomposition' argument no function
+    expect_error( identifySignatures(sca_mm, 3, "a"),
+                 "*.must be a function.*")
+
+    ## 'x' no matrix
+    expect_error( identifySignatures(1:10, 3) )
+})
+
+
+context("assessNumberSignatures")
+
+test_that("'assessNumberSignatures' works", {
+
+    data("sca_mm", package = "SomaticSignatures")
+
+    gof_nmf = assessNumberSignatures(sca_mm, 2:4)
+    expect_is( gof_nmf, "data.frame" )
+
+    gof_pca = assessNumberSignatures(sca_mm, 2:4, pcaDecomposition)
+    expect_is( gof_pca, "data.frame" )
+})
+
+test_that("'assessNumberSignatures' low-level functions work", {
+
+    x = matrix(rnorm(100, 20))
+    y = matrix(rnorm(100, 20))
+
+    library(NMF)
+
+    r1 = rss(x, y)
+    e1 = evar(x, y)
+    expect_true( r1 > 0 )
+    expect_true( e1 <= 1 )
+
+    r1 = rss(x, x)
+    e1 = evar(x, x)
+    expect_equal( r1, 0 )
+    expect_equal( e1, 1 )
+})