Merge pull request #38 from rformassspectrometry/jomain

Fix subset with negative indices

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsExperiment
 Title: Infrastructure for Mass Spectrometry Experiments
-Version: 1.1.4
+Version: 1.5.1
 Description: Infrastructure to store and manage all aspects related to
    a complete proteomics or metabolomics mass spectrometry (MS)
    experiment. The MsExperiment package provides light-weight and

NEWS.md

@@ -1,3 +1,9 @@
+# MsExperiment 1.5
+
+## MsExperiment 1.5.1
+
+- Fix subset with negative indices ([issue #37](https://github.com/rformassspectrometry/MsExperiment/issues/37).)
+
 # MsExperiment 1.1
 
 ## MsExperiment 1.1.4

R/MsExperiment.R

@@ -501,5 +501,10 @@ setMethod("[", "MsExperiment", function(x, i, j, ..., drop = FALSE) {
                  "samples in 'x'.")
         i <- which(i)
     }
+    if (any(i < 0)) {
+        if (all(i < 0))
+            i <- seq_along(x)[i]
+        else stop("Mixing positive and negative indices is not supported.")
+    }
     .extractSamples(x, i, newx = x)
 })

tests/testthat/test_MsExperiment.R

@@ -109,6 +109,35 @@ test_that("[,LinkedMsExperiment works", {
     qdata(mse2) <- se[, 1:2]
     res <- mse2[1:2]
     expect_equal(res, mse2)
+
+    ## Subsetting with negative indices
+    msel <- mse
+    spectra(msel)$mzML_file <- basename(spectra(msel)$dataOrigin)
+    msel <- linkSampleData(
+        msel, with = "sampleData.mzML_file = spectra.mzML_file")
+    res <- msel[-1]
+    expect_equal(length(res), (length(msel) - 1))
+    expect_equal(sampleData(res)$sample, sampleData(msel)$sample[-1])
+    expect_equal(unique(basename(spectra(res)$dataOrigin)),
+                 unique(basename(spectra(msel)$dataOrigin))[2])
+
+    expect_error(msel[c(1, -2)], "not supported")
+
+    ## Multiple files/samples.
+    sd <- data.frame(sample = c("A", "B", "C"))
+    f <- c(fls, system.file("microtofq", "MM14.mzML", package = "msdata"))
+    msel <- readMsExperiment(spectraFiles = f, sampleData = sd)
+    res <- msel[-2]
+    expect_true(length(res) == 2L)
+    expect_equal(sampleData(res)$sample, c("A", "C"))
+    expect_equal(unique(basename(spectra(res)$dataOrigin)),
+                 unique(basename(spectra(msel)$dataOrigin))[c(1, 3)])
+
+    ref <- msel[2]
+    res <- msel[c(-1, -3)]
+    expect_equal(sampleData(ref), sampleData(res))
+    expect_equal(spectra(ref), spectra(res))
+    expect_equal(ref@sampleDataLinks, res@sampleDataLinks)
 })
 
 test_that("MsExperiment works", {