Merge pull request #367 from lgatto/spectra_methods

Spectra methods
lgatto · Oct 24, 2018 · 57fb5db · 57fb5db
2 parents 55058b6 + 4ce04c3
commit 57fb5db
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Showing 16 changed files with 806 additions and 166 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -33,8 +33,9 @@ importFrom(ggplot2, geom_histogram, geom_text, geom_line, geom_point,
            facet_grid)
 
 importFrom(MALDIquant, binPeaks, match.closest) ## only using ::: functions
-importFrom(S4Vectors, isEmpty, metadata, DataFrame, replaceROWS, SimpleList)
-importMethodsFrom(S4Vectors, showAsCell, "mcols<-", mcols, split, endoapply)
+importFrom(S4Vectors, isEmpty, metadata, DataFrame, replaceROWS, SimpleList,
+           endoapply)
+importMethodsFrom(S4Vectors, showAsCell, "mcols<-", mcols, split)
 importClassesFrom(S4Vectors, SimpleList)
 importFrom(MASS, rlm)
 
@@ -146,7 +147,8 @@ export(MSnSet,
        requiredFvarLabels,
        addMSnSetMetadata,
        readSRMData,
-       combineSpectra,
+       meanMzInts,
+       consensusSpectrum,
        combineSpectraMovingWindow,
        estimateMzScattering,
        hasSpectra, hasChromatograms,
@@ -307,7 +309,8 @@ exportMethods(updateObject,
               reduce,
               writeMSData,
               productMz,
-              estimateMzResolution
+              estimateMzResolution,
+	      combineSpectra
               )
 
 ## methods NOT exported

diff --git a/NEWS b/NEWS
@@ -2,6 +2,9 @@
 
 Changes in version 2.7.10
 - Methods for Spectra class <2018-10-15 Mon>
+- Change default for `timeDomain` in `combineSpectra` and 
+  `combineSpectraMovingWindow` to `FALSE` <2018-10-18 Thu>
+- Add new spectra combination function `consensusSpectrum` <2018-10-24 Wed>
 
 Changes in version 2.7.9
 - Import rather than depend on BiocParallel <2018-10-15 Mon>

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,9 @@
 
 ## Changes in version 2.7.10
 - Methods for Spectra class <2018-10-15 Mon>
+- Change default for `timeDomain` in `combineSpectra` and 
+  `combineSpectraMovingWindow` to `FALSE` <2018-10-18 Thu>
+- Add new spectra combination function `consensusSpectrum` <2018-10-24 Wed>
 
 ## Changes in version 2.7.9
 - Import rather than depend on BiocParallel <2018-10-15 Mon>

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -151,3 +151,6 @@ setGeneric("productMz", function(object, ...) standardGeneric("productMz"))
 ## centroiding related
 setGeneric("estimateMzResolution", function(object, ...)
     standardGeneric("estimateMzResolution"))
+
+setGeneric("combineSpectra", function(object, ...)
+           standardGeneric("combineSpectra"))
diff --git a/R/functions-MSnExp.R b/R/functions-MSnExp.R
@@ -448,7 +448,7 @@ estimateMzScattering <- function(x, halfWindowSize = 1L, timeDomain = FALSE) {
 #' signal to noise ratio.
 #'
 #' Intensities (and m/z values) for signals with the same m/z value in
-#' consecutive scans are aggregated using the `intensityFun` and `mzFun`. 
+#' consecutive scans are aggregated using the `intensityFun`. 
 #' m/z values of intensities from consecutive scans will never be exactly
 #' identical, even if they represent signal from the same ion. The function
 #' determines thus internally a similarity threshold based on differences
@@ -457,7 +457,7 @@ estimateMzScattering <- function(x, halfWindowSize = 1L, timeDomain = FALSE) {
 #' threshold is estimated on the 100 spectra with the largest number of
 #' m/z - intensity pairs (i.e. mass peaks).
 #' 
-#' See [combineSpectra()] for details.
+#' See [meanMzInts()] for details.
 #'
 #' Parameter `timeDomain`: by default, m/z-intensity pairs from consecutive
 #' scans to be aggregated are defined based on the square root of the m/z
@@ -485,15 +485,15 @@ estimateMzScattering <- function(x, halfWindowSize = 1L, timeDomain = FALSE) {
 #' 
 #' @param BPPARAM parallel processing settings.
 #' 
-#' @inheritParams combineSpectra
+#' @inheritParams meanMzInts
 #'
 #' @return `MSnExp` with the same number of spectra than `x`.
 #'
 #' @md
 #'
 #' @seealso
 #'
-#' [combineSpectra()] for the function combining spectra provided in
+#' [meanMzInts()] for the function combining spectra provided in
 #' a `list`.
 #'
 #' [estimateMzScattering()] for a function to estimate m/z value scattering in
@@ -537,18 +537,18 @@ estimateMzScattering <- function(x, halfWindowSize = 1L, timeDomain = FALSE) {
 #' plot(chr_comb)
 #' ## Chromatographic data is "smoother" after combining.
 combineSpectraMovingWindow <- function(x, halfWindowSize = 1L,
-                                       mzFun = base::mean,
                                        intensityFun = base::mean,
                                        mzd = NULL,
-                                       timeDomain = TRUE,
+                                       timeDomain = FALSE,
+                                       weighted = FALSE,
                                        BPPARAM = bpparam()){
     if (!is(x, "MSnExp"))
         stop("'x' has to be a 'MSnExp' or an 'OnDiskMSnExp'")
     if (is(x, "OnDiskMSnExp"))
         x <- as(x, "MSnExp")
     ## Combine spectra per file
     new_sp <- bplapply(split(spectra(x), fromFile(x)), FUN = function(z, intF,
-                                                                      mzF, hws,
+                                                                      wght, hws,
                                                                       mzd,
                                                                       timeD) {
         len_z <- length(z)
@@ -566,13 +566,14 @@ combineSpectraMovingWindow <- function(x, halfWindowSize = 1L,
         res <- vector("list", len_z)
         hwsp <- hws + 1L
         for (i in seq_along(z)) {
-            res[[i]] <- combineSpectra(z[windowIndices(i, hws, len_z)],
-                                       mzFun = mzF, intensityFun = intF,
+            res[[i]] <- meanMzInts(z[windowIndices(i, hws, len_z)],
+                                       weighted = wght, intensityFun = intF,
                                        main = hwsp - (i <= hws) * (hwsp - i),
-                                       mzd = mzd, timeDomain = timeD)
+                                       mzd = mzd, timeDomain = timeD,
+                                       unionPeaks = FALSE)
         }
         res
-    }, intF = intensityFun, mzF = mzFun, hws = as.integer(halfWindowSize),
+    }, intF = intensityFun, wght = weighted, hws = as.integer(halfWindowSize),
     mzd = mzd, timeD = timeDomain, BPPARAM = BPPARAM)
     new_sp <- unsplit(new_sp, fromFile(x))
     names(new_sp) <- featureNames(x)