Add filterMsLevel,Spectra and coerce,Spectra,MSnExp

- Add filterMsLevel,Spectra method. - Add coerce,Spectra,MSnExp method (issue #370). - Add related unit tests and documentation.
lgatto · Nov 7, 2018 · f889296 · f889296
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diff --git a/NEWS b/NEWS
@@ -4,6 +4,7 @@ Changes in version 2.9.1
 - Add clean,Chromatograms (issue #354) <2018-11-07 Wed>
 - Add as,Spectra,list as,Spectra,MSnExp and as,MSnExp,Spectra (issue #370)
   <2018-11-07 Wed>
+- Add filterMsLevel,Spectra <2018-11-07 Wed>
 
 Changes in version 2.9.0
 - New version for Bioc 3.9 devel

diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,7 @@
   [#354](https://github.com/lgatto/MSnbase/issues/354)) <2018-11-07 Wed>
 - Add as,Spectra,list as,Spectra,MSnExp and as,MSnExp,Spectra
   (issue [#370](https://github.com/lgatto/MSnbase/issues/370)) <2018-11-07 Wed>
+- Add filterMsLevel,Spectra <2018-11-07 Wed>
 
 ## Changes in version 2.9.0
 - New version for Bioc 3.9 devel

diff --git a/R/DataClasses.R b/R/DataClasses.R
@@ -523,9 +523,9 @@ setClass("ProcessingStep",
 #'     example, a \code{Chromatogram} for a SRM transition 273 -> 153 will have
 #'     a \code{@precursorMz = c(273, 273)} and a
 #'     \code{@productMz = c(153, 153)}.
-#' 
+#'
 #' @rdname Chromatogram-class
-#' 
+#'
 #' @export
 #'
 #' @seealso \code{\link{Chromatograms}} for combining \code{Chromatogram} in
@@ -535,7 +535,7 @@ setClass("ProcessingStep",
 #'     object.
 #'     \code{\link{clean}} for the method to \emph{clean} a \code{Chromatogram}
 #'     object.
-#' 
+#'
 #' @author Johannes Rainer
 #'
 #' @examples
@@ -588,7 +588,7 @@ setClass("Chromatogram",
 #' @title Container for multiple Chromatogram objects
 #'
 #' @aliases coerce,matrix,Chromatograms-method
-#' 
+#'
 #' @description The \code{Chromatograms} class allows to store
 #'     \code{\link{Chromatogram}} objects in a \code{matrix}-like
 #'     two-dimensional structure.
@@ -611,9 +611,9 @@ setClass("Chromatogram",
 #'     \code{\linkS4class{OnDiskMSnExp}} object.
 #'     \code{\link{readSRMData}} for the function to read chromatographic data
 #'     of an SRM/MRM experiment.
-#' 
+#'
 #' @author Johannes Rainer
-#' 
+#'
 #' @examples
 #' ## Creating some chromatogram objects to put them into a Chromatograms object
 #' ints <- abs(rnorm(25, sd = 200))
@@ -676,8 +676,8 @@ setClass("Chromatograms",
 
 #' @name Spectra
 #'
-#' @aliases Spectra-class show,Spectra-method coerce,Spectra,list-method
-#' 
+#' @aliases Spectra-class show,Spectra-method coerce,Spectra,list-method coerce,Spectra,MSnExp-method
+#'
 #' @title List of Spectrum objects along with annotations
 #'
 #' @description
@@ -688,7 +688,7 @@ setClass("Chromatograms",
 #' `Spectrum` object. These can be accessed/set with the [mcols()] method.
 #'
 #' `Spectra` objects can be created with the `Spectra` function.
-#' 
+#'
 #' Functions to access the individual spectra's attributes are available
 #' (listed below).
 #'
@@ -701,7 +701,7 @@ setClass("Chromatograms",
 #' @param object For all functions: a `Spectra` object.
 #'
 #' @param x For all functions: a `Spectra` object.
-#' 
+#'
 #' @md
 #'
 #' @rdname Spectra

diff --git a/R/methods-Spectra.R b/R/methods-Spectra.R
@@ -61,9 +61,6 @@ setMethod("show", "Spectra", function(object) {
 #'
 #' - `clean` *cleans* each spectrum. See [clean()] for more details.
 #'
-#' - `filterMz` filters the spectra by the specified `mz` range. See
-#'   [filterMz()] for details.
-#'
 #' - `pickPeaks` performs peak picking to generate centroided spectra. See
 #'   [pickPeaks()] for more details.
 #'
@@ -72,13 +69,25 @@ setMethod("show", "Spectra", function(object) {
 #'
 #' - `smooth` *smooths* spectra. See [smooth()] for more details.
 #'
+#' @section Filtering and subsetting
+#'
+#' - `[` can be used to subset the `Spectra` object.
+#'
+#' - `filterMsLevel` filters `Spectra` to retain only spectra from certain MS
+#'   level(s).
+#'
+#' - `filterMz` filters the spectra by the specified `mz` range. See
+#'   [filterMz()] for details.
+#'
+#'
 #' @md
 #'
 #' @param all For `clean`: if `FALSE` original 0-intensity values are retained
 #'   around peaks.
 #'
 #' @param msLevel. For `clean`, `removePeaks`, `filterMz`: optionally specify
 #'   the MS level of the spectra on which the operation should be performed.
+#'   For `filterMsLevels`: MS level(s) to which the `Spectra` should be reduced.
 #'
 #' @param method For `pickPeaks` and `smooth`: see [pickPeaks()] and [smooth()]
 #'   for details.
@@ -518,12 +527,40 @@ setAs("Spectra", "list", function(from) {
     from@listData
 })
 
-## setAs("Spectra", "MSnExp", function(from) {
-##     ## mcols -> featureData
-##     ## empty phenoData
-##     ## empty processing
-##     ## spectra -> spectra
-## })
+setAs("Spectra", "MSnExp", function(from) {
+    if (length(unique(msLevel(from))) > 1)
+        stop("'from' contains Spectra from more than one MS level. Use ",
+             "'filterMsLevel' to restrict to Spectra from a single MS level ",
+             "before coercing.")
+    if (!length(names(from)))
+        names(from) <- as.character(seq_len(length(from)))
+    if (is.null(mcols(from)))
+        fd <- AnnotatedDataFrame(data.frame(spectrum = seq_len(length(from)),
+                                            row.names = names(from)))
+    else
+        fd <- AnnotatedDataFrame(as.data.frame(mcols(from)))
+    fromf <- as.character(unique(fromFile(from)))
+    process <- new("MSnProcess", files = fromf,
+                   processing = paste("Data converted from Spectra:", date()))
+    pd <- data.frame(sampleNames = fromf)
+    assaydata <- list2env(as(from, "list"))
+    lockEnvironment(assaydata, bindings = TRUE)
+    new("MSnExp", assayData = assaydata,
+        phenoData = new("NAnnotatedDataFrame", pd), featureData = fd,
+        processingData = process)
+})
+
+#' @rdname Spectra
+#'
+#' @examples
+#'
+#' ## Filter the object by MS level
+#' filterMsLevel(spl, msLevel. = 1)
+setMethod("filterMsLevel", "Spectra", function(object, msLevel.) {
+    if (missing(msLevel.)) return(object)
+    msLevel. <- as.numeric(msLevel.)
+    object[msLevel(object) %in% msLevel.]
+})
 
 ## Still to implement:
 ## quantify, method = c("trapezoidation", "max", "sum", reporters, strict = FALSE)

diff --git a/man/Spectra.Rd b/man/Spectra.Rd
diff --git a/tests/testthat/test_methods-Spectra.R b/tests/testthat/test_methods-Spectra.R
@@ -12,15 +12,15 @@ test_that("mz, intensity, rtime work", {
     expect_true(length(mz(spl)) == 3)
     expect_equal(mz(spl[[2]]), mz(spl)[[2]])
     expect_equal(mz(spl)[[3]], mz(sp3))
-    
+
     expect_true(length(intensity(spl)) == 3)
     expect_equal(intensity(spl[[2]]), intensity(spl)[[2]])
     expect_equal(intensity(spl)[[3]], intensity(sp3))
-    
+
     expect_true(length(rtime(spl)) == 3)
     expect_equal(rtime(spl[[2]]), rtime(spl)[[2]])
     expect_equal(rtime(spl)[[3]], rtime(sp3))
-    
+
     spl <- c(spl, Spectra(new("Spectrum2")))
     expect_true(lengths(mz(spl))[4] == 0)
     expect_true(lengths(intensity(spl))[4] == 0)
@@ -53,7 +53,7 @@ test_that("precursor* work", {
     expect_equal(precursorIntensity(spl), c(1234.4, NA, NA))
     expect_equal(precScanNum(spl), c(NA_integer_, 34L, NA_integer_))
     expect_true(is.integer(precScanNum(spl)))
-    
+
     expect_equal(precursorMz(spl_), c(NA_real_, 2, NA_real_))
     expect_equal(precursorCharge(spl_), rep(NA_integer_, length(spl_)))
     expect_equal(precursorIntensity(spl_), rep(NA_real_, length(spl_)))
@@ -66,7 +66,7 @@ test_that("acquisitionNum and scanIndex work", {
     spl <- Spectra(sp1, sp2)
     expect_identical(acquisitionNum(spl), c(2L, 4L))
     expect_identical(scanIndex(spl), c(1L, NA_integer_))
-        
+
     expect_equal(acquisitionNum(spl_), rep(NA_integer_, length(spl_)))
     expect_equal(scanIndex(spl_), rep(NA_integer_, length(spl_)))
     expect_true(is.integer(acquisitionNum(spl_)))
@@ -199,7 +199,7 @@ test_that("removePeaks,Spectra works", {
     res_2 <- lapply(spl, removePeaks)
     expect_equal(res@listData, res_2)
     expect_equal(mcols(res)$id, 1:3)
-    
+
     res <- removePeaks(spl, t = 10, msLevel. = 1)
     expect_true(is(res, "Spectra"))
     res_2 <- lapply(spl, removePeaks, t = 10, msLevel. = 1)
@@ -253,7 +253,7 @@ test_that("combineSpectra,Spectra works", {
     ints2[11:20] <- c(15, 30, 60, 120, 300, 200, 90, 60, 30, 23)
     ints3 <- abs(rnorm(length(mzs), 10))
     ints3[11:20] <- c(13, 20, 50, 100, 200, 100, 80, 40, 30, 20)
-    
+
     ## Create the spectra.
     sp1 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.01),
                intensity = ints1, rt = 1)
@@ -263,7 +263,7 @@ test_that("combineSpectra,Spectra works", {
                intensity = ints3, rt = 3)
     sp4 <- new("Spectrum2", mz = 1:3, intensity = c(4, 8, 1))
     sp5 <- new("Spectrum2", mz = 2:4, intensity = c(5, 8, 2))
-    
+
     spctra <- Spectra(sp1, sp2, sp3,
                       elementMetadata = DataFrame(idx = 1:3,
                                                   group = c("b", "a", "a")))
@@ -275,15 +275,15 @@ test_that("combineSpectra,Spectra works", {
 
     names(spctra) <- c("A", "B", "C")
     res <- combineSpectra(spctra)
-    
+
     expect_error(combineSpectra(spctra, fcol = "other"))
     res <- combineSpectra(spctra, fcol = "group", mzd = 0.05)
     expect_equal(lengths(intensity(res)), c(b = 191, a = 191))
     expect_equal(names(res), c("b", "a"))
     expect_equal(res[[1]], sp1)
     expect_equal(mcols(res), DataFrame(idx = c(1, 2), group = c("b", "a"),
                                        row.names = c("b", "a")))
-    
+
     spctra <- Spectra(sp1, sp2, sp3, sp4, sp5,
                       elementMetadata = DataFrame(group = c("a", "b", "a",
                                                             "c", "c")))
@@ -295,3 +295,53 @@ test_that("combineSpectra,Spectra works", {
     expect_equal(msLevel(res), c(a = 1, b = 1, c = 2))
     expect_equal(intensity(res)[[3]], c(4, mean(c(8, 5)), mean(c(1, 8)), 2))
 })
+
+test_that("as,Spectra,list works", {
+    sps <- Spectra()
+    res <- as(sps, "list")
+    expect_true(length(res) == 0)
+    expect_true(is.list(res))
+
+    res <- as(spl_, "list")
+    expect_true(is.list(res))
+    expect_equal(res, list(sp1, sp2, sp3))
+})
+
+test_that("as,Spectra,MSnExp works", {
+    sps <- Spectra()
+    res <- as(sps, "MSnExp")
+    expect_true(is(res, "MSnExp"))
+    expect_true(length(res) == 0)
+    expect_true(validObject(res))
+
+    expect_error(as(spl_, "MSnExp"))
+    spl_2 <- filterMsLevel(spl_, 2)
+    res <- as(spl_2, "MSnExp")
+    expect_equal(unname(spectra(res)), as(spl_2, "list"))
+    res <- as(spl_2[2:1], "MSnExp")
+    expect_equal(unname(spectra(res)), as(spl_2[2:1], "list"))
+    mcols(spl_2) <- DataFrame(id = c("a", "b"), other = c("d", "e"))
+    res <- as(spl_2, "MSnExp")
+    expect_equal(fData(res)$id, mcols(spl_2)$id)
+    expect_equal(fData(res)$other, mcols(spl_2)$other)
+    expect_equal(unname(spectra(res)), as(spl_2, "list"))
+
+    spl_1 <- filterMsLevel(spl_, 1)
+    res <- as(spl_1, "MSnExp")
+    expect_equal(spectra(res), list(`1` = sp3))
+})
+
+test_that("filterMsLevel,Spectra works", {
+    res <- filterMsLevel(spl_, 1)
+    expect_equal(res, Spectra(sp3))
+
+    expect_equal(filterMsLevel(spl_), spl_)
+    expect_equal(filterMsLevel(spl_, 1:4), spl_)
+
+    res <- filterMsLevel(spl_, 2)
+    expect_equal(res, Spectra(sp1, sp2))
+
+    res <- filterMsLevel(spl_, 4)
+    expect_true(is(res, "Spectra"))
+    expect_true(length(res) == 0)
+})