fix: selectSpectraVariables to not drop peaks variables

- Ensure `selectSpectraVariables()` for `MsBackendMzR` is not removing peaks variables `"mz"` and `"intensity"` by default.
rformassspectrometry · Jul 23, 2024 · d0ea0b1 · d0ea0b1
1 parent 681f27d
commit d0ea0b1
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Showing 5 changed files with 34 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.15.5
+Version: 1.15.6
 Description: The Spectra package defines an efficient infrastructure
    for storing and handling mass spectrometry spectra and functionality to
    subset, process, visualize and compare spectra data. It provides different

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # Spectra 1.15
 
+## Changes in 1.15.6
+
+- Fix in `selectSpectraVariables()` for `MsBackendMzR`: ensure peaks variables
+  `"mz"` and `"intensity"` are not by default removed.
+
 ## Changes in 1.15.5
 
 - Add new `filterPeaksRanges()` function to filter mass peaks by ranges on

diff --git a/R/MsBackendDataFrame.R b/R/MsBackendDataFrame.R
@@ -406,15 +406,15 @@ setMethod("selectSpectraVariables", "MsBackendDataFrame",
                                                 spectraVariables(object))],
                              collapse = ", "), " not available")
               keep <- spectraVariables[spectraVariables %in%
-                                            colnames(object@spectraData)]
+                                       colnames(object@spectraData)]
               if (length(keep))
                   object@spectraData <- object@spectraData[, keep,
                                                            drop = FALSE]
               msg <- .valid_spectra_data_required_columns(object@spectraData)
               if (length(msg))
                   stop(msg)
               object@peaksVariables <- intersect(object@peaksVariables,
-                                                 colnames(object@spectraData))
+                                                 spectraVariables)
               validObject(object)
               object
 })

diff --git a/tests/testthat/test_MsBackendDataFrame.R b/tests/testthat/test_MsBackendDataFrame.R
@@ -622,15 +622,32 @@ test_that("selectSpectraVariables,MsBackendDataFrame works", {
     be <- backendInitialize(MsBackendDataFrame(), df)
 
     res <- selectSpectraVariables(be, c("dataStorage", "other_col"))
+
+    expect_equal(res@peaksVariables, be@peaksVariables)
     expect_equal(colnames(res@spectraData), c("dataStorage", "other_col"))
     expect_equal(msLevel(res), c(NA_integer_, NA_integer_))
 
     res <- selectSpectraVariables(be, c("dataStorage", "rtime"))
     expect_equal(colnames(res@spectraData), c("dataStorage", "rtime"))
+    expect_equal(res@peaksVariables, be@peaksVariables)
 
     expect_error(selectSpectraVariables(be, "rtime"), "dataStorage is/are missing")
     expect_error(selectSpectraVariables(be, "something"),
                  "something not available")
+
+    df$mz <- list(c(1.2, 1.4), c(5.3, 34.5, 52.1))
+    df$intensity <- list(c(123, 121.1), c(1231.1, 343.1, 21.1))
+    be <- backendInitialize(MsBackendDataFrame(), df)
+    res <- selectSpectraVariables(be, c("dataStorage", "other_col"))
+    expect_equal(colnames(res@spectraData), c("dataStorage", "other_col"))
+    expect_equal(msLevel(res), c(NA_integer_, NA_integer_))
+    expect_equal(res@peaksVariables, character())
+
+    be <- backendInitialize(MsBackendDataFrame(), df)
+    res <- selectSpectraVariables(be, c("dataStorage", "mz", "intensity"))
+    expect_equal(colnames(res@spectraData), c("dataStorage", "mz", "intensity"))
+    expect_equal(msLevel(res), c(NA_integer_, NA_integer_))
+    expect_equal(res@peaksVariables, c("mz", "intensity"))
 })
 
 test_that("$,$<-,MsBackendDataFrame works", {

diff --git a/tests/testthat/test_MsBackendMzR.R b/tests/testthat/test_MsBackendMzR.R
@@ -493,6 +493,14 @@ test_that("selectSpectraVariables,MsBackendMzR works", {
                                         "scanIndex"))
     expect_equal(colnames(res@spectraData), c("dataStorage", "msLevel", "rtime",
                                               "scanIndex"))
+    expect_equal(res@peaksVariables, character())
+
+    res <- selectSpectraVariables(be, c("dataStorage", "msLevel", "rtime",
+                                        "scanIndex", "mz", "intensity"))
+    expect_equal(colnames(res@spectraData), c("dataStorage", "msLevel", "rtime",
+                                              "scanIndex"))
+    expect_equal(res@peaksVariables, c("mz", "intensity"))
+
     expect_error(selectSpectraVariables(be, c("dataStorage", "msLevel")),
                  "scanIndex is/are missing")
 })
@@ -559,6 +567,7 @@ test_that("dropNaSpectraVariables works with MsBackendMzR", {
     expect_equal(mz(res[1]), mz(sciex_mzr[1]))
     expect_true(length(spectraVariables(res)) <
                 length(spectraVariables(sciex_mzr)))
+    expect_equal(res@peaksVariables, sciex_mzr@peaksVariables)
 })
 
 test_that("supportsSetBackend,MsBackendMzR", {