Add some more Spectra methods

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MSnbase
 Title: Base Functions and Classes for Mass Spectrometry and Proteomics
-Version: 2.9.0
+Version: 2.9.1
 Description: MSnbase provides infrastructure for manipulation,
 	     processing and visualisation of mass spectrometry and
 	     proteomics data, ranging from raw to quantitative and

NEWS

@@ -1,5 +1,11 @@
 # MSnbase 2.9
 
+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
 
@@ -20,7 +26,7 @@ Changes in version 2.7.12
 
 
 Changes in version 2.7.11
-- Change default for `timeDomain` in `combineSpectra` and 
+- Change default for `timeDomain` in `combineSpectra` and
   `combineSpectraMovingWindow` to `FALSE` <2018-10-18 Thu>
 - Add new spectra combination function `consensusSpectrum`
   <2018-10-24 Wed>

NEWS.md

@@ -1,5 +1,12 @@
 # MSnbase 2.9
 
+## Changes in version 2.9.1
+- Add clean,Chromatograms (issue
+  [#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
 
@@ -20,7 +27,7 @@
 
 
 ## Changes in version 2.7.11
-- Change default for `timeDomain` in `combineSpectra` and 
+- Change default for `timeDomain` in `combineSpectra` and
   `combineSpectraMovingWindow` to `FALSE` <2018-10-18 Thu>
 - Add new spectra combination function `consensusSpectrum`
   <2018-10-24 Wed>

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))
@@ -676,7 +676,7 @@ setClass("Chromatograms",
 
 #' @name Spectra
 #'
-#' @aliases Spectra-class show,Spectra-method
+#' @aliases Spectra-class show,Spectra-method coerce,Spectra,list-method coerce,Spectra,MSnExp-method
 #'
 #' @title List of Spectrum objects along with annotations
 #'
@@ -687,6 +687,8 @@ setClass("Chromatograms",
 #' the possibility to add arbitrary annotations to each individual
 #' `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).
 #'
@@ -699,7 +701,7 @@ setClass("Chromatograms",
 #' @param object For all functions: a `Spectra` object.
 #'
 #' @param x For all functions: a `Spectra` object.
-#' 
+#'
 #' @md
 #'
 #' @rdname Spectra

R/functions-Chromatograms.R

@@ -39,11 +39,11 @@
 #'
 #' @param featureData either a \code{data.frame} or \code{AnnotatedDataFrame}
 #'     with additional information for each row of chromatograms.
-#' 
+#'
 #' @param ... Additional parameters to be passed to the
 #'     \code{\link[base]{matrix}} constructor, such as \code{nrow}, \code{ncol}
 #'     and \code{byrow}.
-#' 
+#'
 #' @rdname Chromatograms-class
 Chromatograms <- function(data, phenoData, featureData, ...) {
     if (missing(data))
@@ -112,7 +112,7 @@ Chromatograms <- function(data, phenoData, featureData, ...) {
     ## to the number of data points that were actually measured.
     lens <- lengths(x)
     maxLens <- max(lens)
-    
+
     ints <- rts <- matrix(NA_real_, nrow = maxLens, ncol = length(x))
     for (i in seq(along = x)) {
         if (lens[i]) {
@@ -180,7 +180,7 @@ Chromatograms <- function(data, phenoData, featureData, ...) {
 #' `Chromatogram` objects in each row.
 #'
 #' @author Johannes Rainer
-#' 
+#'
 #' @noRd
 .bin_Chromatograms <- function(object, binSize = 0.5, breaks = numeric(),
                                fun = max) {
@@ -196,4 +196,3 @@ Chromatograms <- function(data, phenoData, featureData, ...) {
     if (validObject(object))
         object
 }
-

R/methods-Chromatograms.R

@@ -28,7 +28,7 @@ setMethod("show", "Chromatograms", function(object) {
         }
         rn <- rownames(out)
         out <- rbind(rep("<Chromatogram>", ncol(out)), out)
-        rownames(out) <- c("", rn)        
+        rownames(out) <- c("", rn)
         print(out, quote = FALSE, right = TRUE)
     }
     cat("phenoData with", length(varLabels(object@phenoData)), "variables\n")
@@ -55,9 +55,9 @@ setAs("matrix", "Chromatograms", function(from) {
 #'     object (with the exception of extracting a single element)
 #'     unless \code{drop = TRUE} is specified. This is different from the
 #'     default subsetting behaviour of \code{matrix}-like objects.
-#' 
+#'
 #' @param x For all methods: a \code{Chromatograms} object.
-#' 
+#'
 #' @param i For \code{[}: \code{numeric}, \code{logical} or \code{character}
 #'     defining which row(s) to extract.
 #'
@@ -123,7 +123,7 @@ setMethod("[", "Chromatograms",
 #' @param value For \code{[<-}: the replacement object(s). Can be a \code{list}
 #'     of \code{\link{Chromatogram}} objects or, if length of \code{i} and
 #'     \code{j} are 1, a single \code{\link{Chromatogram}} object.
-#' 
+#'
 #'     For \code{pData<-}: a \code{data.frame} with the number of rows matching
 #'     the number of columns of \code{object}.
 #'
@@ -163,7 +163,7 @@ setReplaceMethod("[", "Chromatograms",
                  })
 
 #' @rdname Chromatograms-class
-#' 
+#'
 #' @description \code{plot}: plots a \code{Chromatograms} object. For each row
 #'     in the object one plot is created, i.e. all \code{\link{Chromatogram}}
 #'     objects in the same row are added to the same plot.
@@ -182,11 +182,11 @@ setReplaceMethod("[", "Chromatograms",
 #' @param type For \code{plot}: the type of plot (see
 #'     \code{\link[graphics]{plot}} for more details. Can be either a vector
 #'     of length 1 or of length equal to \code{ncol(x)}.
-#' 
+#'
 #' @inheritParams Chromatogram-class
 #'
 #' @examples
-#' 
+#'
 #' ## Create some random Chromatogram objects
 #' ints <- abs(rnorm(123, mean = 200, sd = 32))
 #' ch1 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 231)
@@ -312,7 +312,7 @@ setMethod("isEmpty", "Chromatograms", function(x) {
 })
 
 #' @rdname Chromatograms-class
-#' 
+#'
 #' @description \code{featureNames}: returns the feature names of the
 #'     \code{Chromatograms} object.
 setMethod("featureNames", "Chromatograms", function(object)
@@ -463,3 +463,26 @@ setMethod("polarity", "Chromatograms", function(object) {
 #'
 #' @rdname Chromatograms-class
 setMethod("bin", "Chromatograms", .bin_Chromatograms)
+
+#' @description
+#'
+#' \code{clean}: removes 0-intensity data points. Either all of them
+#' (with \code{all = TRUE}) or all except those adjacent to non-zero
+#' intensities (\code{all = FALSE}; default). See \code{\link{clean}}
+#' documentation for more details and examples.
+#'
+#' @param all for \code{clean}: \code{logical(1)} whether all 0 intensities
+#'     should be removed (\code{all = TRUE}), or whether 0-intensities
+#'     adjacent to peaks should be kept (\code{all = FALSE}; default).
+#'
+#' @param na.rm for \code{clean}: \code{logical(1)} whether all \code{NA}
+#'     intensities should be removed prior to clean 0 intensity data points.
+#'
+#' @rdname Chromatograms-class
+setMethod("clean", "Chromatograms", function(object, all = FALSE,
+                                             na.rm = FALSE) {
+    [email protected] <- matrix(lapply(object, clean, all = all, na.rm = na.rm),
+                           nrow = nrow(object), dimnames = dimnames(object))
+    if (validObject(object))
+        object
+})

R/methods-MSnExp.R

@@ -565,3 +565,15 @@ setAs("MSnExp", "data.frame", function(from) {
 })
 as.data.frame.MSnExp <- function(x, row.names = NULL, optional=FALSE, ...)
     as(x, "data.frame")
+
+setAs("MSnExp", "Spectra", function(from) {
+    fdta <- fData(from)
+    red_cn <- c("fileIdx", "spIdx", "smoothed", "seqNum", "acquisitionNum",
+                "msLevel", "polarity", "originalPeaksCount", "totIonCurrent",
+                "retentionTime", "basePeakMZ", "basePeakIntensity",
+                "collisionEnergy", "ionisationEnergy", "precursorScanNum",
+                "precursorMZ", "precursorCharge", "precursorIntensity",
+                "mergedScan", "centroided", "spectrum")
+    fdta <- fdta[, !colnames(fdta) %in% red_cn, drop = FALSE]
+    Spectra(spectra(from), elementMetadata = DataFrame(fdta))
+})