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sgibbsgibb
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Merge pull request #72 from sgibb/occurrence-list
Reduced memory requirement for filterPeaks; closes #71
2 parents b1ca2ff + f817438 commit 3d4f73f

9 files changed

Lines changed: 191 additions & 160 deletions

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‎.Rbuildignore‎

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^CRAN-RELEASE$
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^cran-comments.md$
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^\.github$
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^.*\.Rproj$
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^\.Rproj\.user$

‎.gitignore‎

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*.o
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*.rds
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CRAN-RELEASE
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.Rproj.user
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.Rproj

‎DESCRIPTION‎

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@@ -1,12 +1,27 @@
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Package: MALDIquant
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Version: 1.20
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Version: 1.20.0.9999
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Date: 2021-07-29
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Title: Quantitative Analysis of Mass Spectrometry Data
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Authors@R: c(person("Sebastian", "Gibb", role=c("aut", "cre"),
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Authors@R: c(
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person(
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given = "Sebastian", family = "Gibb",
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email="mail@sebastiangibb.de",
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comment=c(ORCID="0000-0001-7406-4443")), person("Korbinian",
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"Strimmer", role="ths",
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comment=c(ORCID="0000-0001-7917-2056")))
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comment=c(ORCID="0000-0001-7406-4443"),
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role = c("aut", "cre")
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),
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person(
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given = "Korbinian", family = "Strimmer",
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comment=c(ORCID="0000-0001-7917-2056"),
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role="ths"
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),
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person(given = "Sigurdur", family = "Smarason", role = "ctb"),
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person(
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given = "Laurent", family = "Gatto",
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email = "laurent.gatto@uclouvain.be",
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comment = c(ORCID = "0000-0002-1520-2268"),
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role = "ctb"
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),
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person(given = "Paolo", "family = Inglese", role = "ctb"))
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Depends: R (>= 4.0.0), methods
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Imports: parallel
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Suggests: knitr, testthat (>= 0.8)
@@ -26,4 +41,4 @@ URL: https://www.strimmerlab.org/software/maldiquant/
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BugReports: https://github.com/sgibb/MALDIquant/issues/
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LazyLoad: yes
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VignetteBuilder: knitr
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RoxygenNote: 7.1.1
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RoxygenNote: 7.1.2

‎NEWS‎

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RELEASE HISTORY OF THE "MALDIquant" PACKAGE
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===========================================
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CHANGES IN MALDIquant VERSION 1.20.0.9999 [unreleased]:
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-------------------------------------------------------
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MODIFICATIONS
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* Reduce memory requirement for `filterPeaks`, especially for very sparse peak
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lists by rewriting `filterPeaks` and `.as.matrix.MassObjectList` to use a
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`list` internally instead of a `matrix`; see #71.
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Contributed by Paolo Inglese <p.inglese@outlook.com> (@paoloinglese).
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INTERNAL CHANGES
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* Remove `is.null(getGeneric(...))` tests before setting generics for
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S4 methods to avoid errors in package loading (especially with
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`pkgload::load_all()`).
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CHANGES IN MALDIquant VERSION 1.20 [2021-07-29]:
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------------------------------------------------
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‎R/AllGenerics.R‎

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## AbstractMassObject
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if (is.null(getGeneric("plotMsiSlice"))) {
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setGeneric("plotMsiSlice", function(x, ...) standardGeneric("plotMsiSlice"))
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}
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if (is.null(getGeneric(".prepareShow"))) {
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setGeneric(".prepareShow", function(object) standardGeneric(".prepareShow"))
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}
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if (is.null(getGeneric("transformIntensity"))) {
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setGeneric("transformIntensity",
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function(object, ...) standardGeneric("transformIntensity"))
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}
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if (is.null(getGeneric(".transformIntensity"))) {
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setGeneric(".transformIntensity",
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function(object, ...) standardGeneric(".transformIntensity"))
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}
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if (is.null(getGeneric("trim"))) {
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setGeneric("trim", function(object, range, ...) standardGeneric("trim"))
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}
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setGeneric("plotMsiSlice", function(x, ...) standardGeneric("plotMsiSlice"))
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setGeneric(".prepareShow", function(object) standardGeneric(".prepareShow"))
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setGeneric(
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"transformIntensity",
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function(object, ...) standardGeneric("transformIntensity")
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)
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setGeneric(
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".transformIntensity",
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function(object, ...) standardGeneric(".transformIntensity")
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)
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setGeneric("trim", function(object, range, ...) standardGeneric("trim"))
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2014
## get/set slots
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if (is.null(getGeneric("mass"))) {
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setGeneric("mass", function(object, ...) standardGeneric("mass"))
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}
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if (is.null(getGeneric("mass<-"))) {
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setGeneric("mass<-", function(object, value) standardGeneric("mass<-"))
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}
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setGeneric("mass", function(object, ...) standardGeneric("mass"))
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setGeneric("mass<-", function(object, value) standardGeneric("mass<-"))
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# from ProtGenerics (same as mass)
28-
if (is.null(getGeneric("mz"))) {
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setGeneric("mz", function(object, ...) standardGeneric("mz"))
30-
}
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if (is.null(getGeneric("mz<-"))) {
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setGeneric("mz<-", function(object, value) standardGeneric("mz<-"))
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}
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if (is.null(getGeneric("intensity"))) {
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setGeneric("intensity", function(object, ...) standardGeneric("intensity"))
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}
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if (is.null(getGeneric("intensity<-"))) {
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setGeneric("intensity<-",
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function(object, value) standardGeneric("intensity<-"))
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}
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if (is.null(getGeneric("isEmpty"))) {
42-
setGeneric("isEmpty", function(x) standardGeneric("isEmpty"))
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}
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if (is.null(getGeneric(".isEmptyWarning"))) {
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setGeneric(".isEmptyWarning", function(x) standardGeneric(".isEmptyWarning"))
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}
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if (is.null(getGeneric("metaData"))) {
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setGeneric("metaData", function(object) standardGeneric("metaData"))
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}
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if (is.null(getGeneric("metaData<-"))) {
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setGeneric("metaData<-",
52-
function(object, value) standardGeneric("metaData<-"))
53-
}
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if (is.null(getGeneric("coordinates"))) {
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setGeneric("coordinates",
56-
function(object, ...) standardGeneric("coordinates"))
57-
}
58-
if (is.null(getGeneric("coordinates<-"))) {
59-
setGeneric("coordinates<-",
60-
function(object, value) standardGeneric("coordinates<-"))
61-
}
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setGeneric("mz", function(object, ...) standardGeneric("mz"))
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setGeneric("mz<-", function(object, value) standardGeneric("mz<-"))
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22+
setGeneric("intensity", function(object, ...) standardGeneric("intensity"))
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setGeneric(
24+
"intensity<-",
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function(object, value) standardGeneric("intensity<-")
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)
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setGeneric("isEmpty", function(x) standardGeneric("isEmpty"))
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setGeneric(".isEmptyWarning", function(x) standardGeneric(".isEmptyWarning"))
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setGeneric("metaData", function(object) standardGeneric("metaData"))
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setGeneric("metaData<-", function(object, value) standardGeneric("metaData<-"))
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setGeneric("coordinates", function(object, ...) standardGeneric("coordinates"))
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setGeneric(
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"coordinates<-",
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function(object, value) standardGeneric("coordinates<-")
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)
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## end of AbstractMassObject
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## MassSpectrum
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if (is.null(getGeneric("calibrateIntensity"))) {
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setGeneric("calibrateIntensity",
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function(object, ...) standardGeneric("calibrateIntensity"))
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}
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if (is.null(getGeneric("detectPeaks"))) {
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setGeneric("detectPeaks",
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function(object, ...) standardGeneric("detectPeaks"))
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}
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if (is.null(getGeneric("estimateBaseline"))) {
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setGeneric("estimateBaseline",
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function(object, method=c("SNIP", "ConvexHull", "Median"), ...)
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standardGeneric("estimateBaseline"))
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}
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if (is.null(getGeneric("estimateNoise"))) {
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setGeneric("estimateNoise",
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function(object, ...) standardGeneric("estimateNoise"))
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}
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if (is.null(getGeneric(".findLocalMaxima"))) {
84-
setGeneric(".findLocalMaxima",
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function(object, halfWindowSize=20L)
86-
standardGeneric(".findLocalMaxima"))
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}
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if (is.null(getGeneric(".findLocalMaximaLogical"))) {
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setGeneric(".findLocalMaximaLogical",
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function(object, halfWindowSize=20L)
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standardGeneric(".findLocalMaximaLogical"))
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}
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if (is.null(getGeneric("isRegular"))) {
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setGeneric("isRegular",
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function(object, ...) standardGeneric("isRegular"))
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}
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if (is.null(getGeneric("removeBaseline"))) {
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setGeneric("removeBaseline",
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function(object, ...) standardGeneric("removeBaseline"))
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}
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if (is.null(getGeneric("smoothIntensity"))) {
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setGeneric("smoothIntensity",
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function(object, ...)
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standardGeneric("smoothIntensity"))
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}
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if (is.null(getGeneric("totalIonCurrent"))) {
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setGeneric("totalIonCurrent",
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function(object) standardGeneric("totalIonCurrent"))
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}
39+
setGeneric(
40+
"calibrateIntensity",
41+
function(object, ...) standardGeneric("calibrateIntensity")
42+
)
43+
setGeneric("detectPeaks", function(object, ...) standardGeneric("detectPeaks"))
44+
setGeneric(
45+
"estimateBaseline",
46+
function(object, method=c("SNIP", "ConvexHull", "Median"), ...)
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standardGeneric("estimateBaseline"))
48+
setGeneric(
49+
"estimateNoise", function(object, ...) standardGeneric("estimateNoise")
50+
)
51+
setGeneric(
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".findLocalMaxima",
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function(object, halfWindowSize=20L) standardGeneric(".findLocalMaxima")
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)
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setGeneric(
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".findLocalMaximaLogical",
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function(object, halfWindowSize=20L)
58+
standardGeneric(".findLocalMaximaLogical")
59+
)
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setGeneric("isRegular", function(object, ...) standardGeneric("isRegular"))
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setGeneric(
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"removeBaseline", function(object, ...) standardGeneric("removeBaseline")
63+
)
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setGeneric(
65+
"smoothIntensity", function(object, ...) standardGeneric("smoothIntensity")
66+
)
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setGeneric(
68+
"totalIonCurrent", function(object) standardGeneric("totalIonCurrent")
69+
)
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## end of MassSpectrum
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## MassPeaks
113-
if (is.null(getGeneric("labelPeaks"))) {
114-
setGeneric("labelPeaks", function(object, ...) standardGeneric("labelPeaks"))
115-
}
116-
if (is.null(getGeneric("monoisotopicPeaks"))) {
117-
setGeneric("monoisotopicPeaks",
118-
function(object, ...) standardGeneric("monoisotopicPeaks"))
119-
}
120-
if (is.null(getGeneric("snr"))) {
121-
setGeneric("snr", function(object) standardGeneric("snr"))
122-
}
73+
setGeneric("labelPeaks", function(object, ...) standardGeneric("labelPeaks"))
74+
setGeneric(
75+
"monoisotopicPeaks",
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function(object, ...) standardGeneric("monoisotopicPeaks")
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)
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setGeneric("snr", function(object) standardGeneric("snr"))
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## end of MassPeaks

‎R/as.list-functions.R‎

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## .as.occurrence.list
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## internal function to create a list of peaks occurrence
3+
##
4+
## params:
5+
## l: list of AbstractMassObject objects
6+
##
7+
## returns:
8+
## a list, where sample is the sample id, i is the index of the uniqueMass,
9+
## and mass is the unique mass vector
10+
.as.occurrence.list.MassObjectList <- function(l) {
11+
.stopIfNotIsMassObjectList(l)
12+
13+
mass <- .unlist(lapply(l, function(x)x@mass))
14+
uniqueMass <- sort.int(unique(mass))
15+
n <- lengths(l)
16+
17+
list(
18+
sample = rep.int(seq_along(l), lengths(l)),
19+
i = findInterval(mass, uniqueMass),
20+
mass = uniqueMass
21+
)
22+
}

‎R/as.matrix-functions.R‎

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88
## returns:
99
## a matrix
1010
.as.matrix.MassObjectList <- function(l) {
11-
.stopIfNotIsMassObjectList(l)
11+
.stopIfNotIsMassObjectList(l)
1212

13-
mass <- .unlist(lapply(l, function(x)x@mass))
14-
intensity <- .unlist(lapply(l, function(x)x@intensity))
15-
uniqueMass <- sort.int(unique(mass))
16-
n <- lengths(l)
17-
r <- rep.int(seq_along(l), n)
13+
intensity <- .unlist(lapply(l, function(x)x@intensity))
14+
o <- .as.occurrence.list.MassObjectList(l)
1815

19-
i <- findInterval(mass, uniqueMass)
20-
21-
m <- matrix(NA_real_, nrow=length(l), ncol=length(uniqueMass),
22-
dimnames=list(NULL, uniqueMass))
23-
m[cbind(r, i)] <- intensity
24-
attr(m, "mass") <- uniqueMass
25-
m
16+
m <- matrix(
17+
NA_real_, nrow=length(l), ncol=length(o$mass),
18+
dimnames=list(NULL, o$mass)
19+
)
20+
m[cbind(o$sample, o$i)] <- intensity
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attr(m, "mass") <- o$mass
22+
m
2623
}
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2825
## .as.binary.matrix
@@ -34,10 +31,9 @@
3431
## returns:
3532
## a binary matrix
3633
.as.binary.matrix <- function(m) {
37-
stopifnot(is.matrix(m))
38-
isNA <- which(is.na(m))
39-
m[] <- 1L
40-
m[isNA] <- 0L
41-
mode(m) <- "integer"
42-
m
34+
if (!is.matrix(m))
35+
stop("'x' has to be a matrix!")
36+
m[] <- !is.na(m)
37+
mode(m) <- "integer"
38+
m
4339
}

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