Merge branch 'main' into filterPrecursorPeaks

NAMESPACE

@@ -21,6 +21,7 @@ export(filterPrecursorMaxIntensity)
 export(filterPrecursorPeaks)
 export(joinPeaks)
 export(joinPeaksGnps)
+export(joinPeaksNone)
 export(joinSpectraData)
 export(plotMzDelta)
 export(plotSpectra)

NEWS.md

@@ -1,10 +1,20 @@
 # Spectra 1.11
 
-## Changes in 1.11.7
+## Changes in 1.11.8
 
 - Add `filterPrecursorPeaks` to allow filtering peaks within each spectrum
   with m/z values relative to the precursor m/z of the spectrum.
 
+## Changes in 1.11.7
+
+- Fix in `compareSpectra` to also pass parameters `ppm` and `tolerance` to
+  the peak similarity calculation functions `FUN`: this allows to use custom
+  similarity function with integrated mapping of peaks.
+- Add `joinPeaksNone` to skip the peak matching in `compareSpectra` if the
+  similarity scoring function performs its own peak matching.
+- Only use parallel processing in `setBackend,Spectra` if both backends support
+  it.
+
 ## Changes in 1.11.6
 
 - Add `filterPrecursorMaxIntensity` function.

R/Spectra-functions.R

@@ -392,7 +392,7 @@ applyProcessing <- function(object, f = dataStorage(object),
                       .check = FALSE,...)
         m[cb[i, 1L], cur] <- m[cur, cb[i, 1L]] <-
             FUN(map[[1L]], map[[2L]], xPrecursorMz = pmzx,
-                yPrecursorMz = pmzy, ...)
+                yPrecursorMz = pmzy, ppm = ppm, tolerance = tolerance, ...)
     }
     m
 }

R/Spectra.R

@@ -623,7 +623,8 @@ NULL
 #'   the spectra's precursor m/z values are passed to the function as parameters
 #'   `xPrecursorMz` (precursor m/z of the `x` peak matrix) and `yPrecursorMz`
 #'   (precursor m/z of the `y` peak matrix). Additional parameters to functions
-#'   `FUN` and `MAPFUN` can be passed with `...`.
+#'   `FUN` and `MAPFUN` can be passed with `...`. Parameters `ppm` and
+#'   `tolerance` are passed to both `MAPFUN` and `FUN`.
 #'   The function returns a `matrix` with the results of `FUN` for each
 #'   comparison, number of rows equal to `length(x)` and number of columns
 #'   equal `length(y)` (i.e. element in row 2 and column 3 is the result from
@@ -1529,6 +1530,7 @@ setMethod(
              BPPARAM = bpparam()) {
         backend_class <- class(object@backend)
         BPPARAM <- backendBpparam(object@backend, BPPARAM)
+        BPPARAM <- backendBpparam(backend, BPPARAM)
         if (!supportsSetBackend(backend))
             stop(class(backend), " does not support 'setBackend'")
         if (!length(object)) {
@@ -1538,7 +1540,7 @@ setMethod(
             f <- force(factor(f, levels = unique(f)))
             if (length(f) != length(object))
                 stop("length of 'f' has to match the length of 'object'")
-            if (length(levels(f)) == 1L) {
+            if (length(levels(f)) == 1L || inherits(BPPARAM, "SerialParam")) {
                 bknds <- backendInitialize(
                     backend, data = spectraData(object@backend), ...)
             } else {

R/peak-list-functions.R

@@ -278,7 +278,8 @@ combinePeaksData <- function(x, intensityFun = base::mean,
                                .check = FALSE, ...)
             mat[i, j] <- FUN(peak_map[[1L]], peak_map[[2L]],
                              xPrecursorMz = xPrecursorMz[i],
-                             yPrecursorMz = yPrecursorMz[j], ...)
+                             yPrecursorMz = yPrecursorMz[j],
+                             ppm = ppm, tolerance = tolerance, ...)
         }
     }
     mat

R/peaks-functions.R

@@ -236,7 +236,7 @@ NULL
 #'   between `x` and `y` are returned by `type = "inner"`, i.e. only
 #'   peaks present in both spectra are reported.
 #'
-#' - `joinPeaksGnps` matches/maps peaks between spectra with the same approach
+#' - `joinPeaksGnps`: matches/maps peaks between spectra with the same approach
 #'   used in GNPS: peaks are considered matching if a) the
 #'   difference in their m/z values is smaller than defined by `tolerance`
 #'   and `ppm` (this is the same as `joinPeaks`) **and** b) the difference of
@@ -250,6 +250,12 @@ NULL
 #'   `compareSpectra` should be called with `MAPFUN = joinPeaksGnps` and
 #'   `FUN = MsCoreUtils::gnps`).
 #'
+#' - `joinPeaksNone`: does not perform any peak matching but simply returns
+#'   the peak matrices in a `list`. This function should be used with the
+#'   `MAPFUN` parameter of [compareSpectra()] if the spectra similarity
+#'   function used (parameter `FUN` of `compareSpectra`) performs its own
+#'   peak matching and does hence not expect matched peak matrices as an input.
+#'
 #' @section Implementation notes:
 #'
 #' A mapping function must take two numeric matrices `x` and `y` as input and
@@ -363,6 +369,13 @@ joinPeaksGnps <- function(x, y, xPrecursorMz = NA_real_,
     list(x = x[map[[1L]], , drop = FALSE], y = y[map[[2L]], , drop = FALSE])
 }
 
+#' @export
+#'
+#' @rdname joinPeaks
+joinPeaksNone <- function(x, y, ...) {
+    list(x = x, y = y)
+}
+
 #' @importFrom MsCoreUtils localMaxima noise refineCentroids
 #'
 #' @description

tests/testthat/test_peaks-functions.R

@@ -101,6 +101,16 @@ test_that(".peaks_bin works", {
     expect_equal(res[, 2], c(1, 5, 1, 0, 1, 13, 8, 1, 3, 0, 6, 15, 1, 0, 0))
 })
 
+test_that("joinPeaksNone works", {
+    x <- cbind(c(31.34, 50.14, 60.3, 120.9, 230, 514.13, 874.1),
+               1:7)
+    y <- cbind(c(12, 31.35, 70.3, 120.9 + ppm(120.9, 5),
+                 230 + ppm(230, 10), 315, 514.14, 901, 1202),
+               1:9)
+    res <- joinPeaksNone(x, y, ppm = 20)
+    expect_equal(res, list(x = x, y = y))
+})
+
 test_that("joinPeaks works", {
     x <- cbind(c(31.34, 50.14, 60.3, 120.9, 230, 514.13, 874.1),
                1:7)