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Merge pull request #72 from sgibb/occurrence-list
Reduced memory requirement for filterPeaks; closes #71
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| ^CRAN-RELEASE$ | ||
| ^cran-comments.md$ | ||
| ^\.github$ | ||
| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
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| *.o | ||
| *.rds | ||
| CRAN-RELEASE | ||
| .Rproj.user | ||
| .Rproj | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,123 +1,79 @@ | ||
| ## AbstractMassObject | ||
| if (is.null(getGeneric("plotMsiSlice"))) { | ||
| setGeneric("plotMsiSlice", function(x, ...) standardGeneric("plotMsiSlice")) | ||
| } | ||
| if (is.null(getGeneric(".prepareShow"))) { | ||
| setGeneric(".prepareShow", function(object) standardGeneric(".prepareShow")) | ||
| } | ||
| if (is.null(getGeneric("transformIntensity"))) { | ||
| setGeneric("transformIntensity", | ||
| function(object, ...) standardGeneric("transformIntensity")) | ||
| } | ||
| if (is.null(getGeneric(".transformIntensity"))) { | ||
| setGeneric(".transformIntensity", | ||
| function(object, ...) standardGeneric(".transformIntensity")) | ||
| } | ||
| if (is.null(getGeneric("trim"))) { | ||
| setGeneric("trim", function(object, range, ...) standardGeneric("trim")) | ||
| } | ||
| setGeneric("plotMsiSlice", function(x, ...) standardGeneric("plotMsiSlice")) | ||
| setGeneric(".prepareShow", function(object) standardGeneric(".prepareShow")) | ||
| setGeneric( | ||
| "transformIntensity", | ||
| function(object, ...) standardGeneric("transformIntensity") | ||
| ) | ||
| setGeneric( | ||
| ".transformIntensity", | ||
| function(object, ...) standardGeneric(".transformIntensity") | ||
| ) | ||
| setGeneric("trim", function(object, range, ...) standardGeneric("trim")) | ||
|
|
||
| ## get/set slots | ||
| if (is.null(getGeneric("mass"))) { | ||
| setGeneric("mass", function(object, ...) standardGeneric("mass")) | ||
| } | ||
| if (is.null(getGeneric("mass<-"))) { | ||
| setGeneric("mass<-", function(object, value) standardGeneric("mass<-")) | ||
| } | ||
| setGeneric("mass", function(object, ...) standardGeneric("mass")) | ||
| setGeneric("mass<-", function(object, value) standardGeneric("mass<-")) | ||
|
|
||
| # from ProtGenerics (same as mass) | ||
| if (is.null(getGeneric("mz"))) { | ||
| setGeneric("mz", function(object, ...) standardGeneric("mz")) | ||
| } | ||
| if (is.null(getGeneric("mz<-"))) { | ||
| setGeneric("mz<-", function(object, value) standardGeneric("mz<-")) | ||
| } | ||
| if (is.null(getGeneric("intensity"))) { | ||
| setGeneric("intensity", function(object, ...) standardGeneric("intensity")) | ||
| } | ||
| if (is.null(getGeneric("intensity<-"))) { | ||
| setGeneric("intensity<-", | ||
| function(object, value) standardGeneric("intensity<-")) | ||
| } | ||
| if (is.null(getGeneric("isEmpty"))) { | ||
| setGeneric("isEmpty", function(x) standardGeneric("isEmpty")) | ||
| } | ||
| if (is.null(getGeneric(".isEmptyWarning"))) { | ||
| setGeneric(".isEmptyWarning", function(x) standardGeneric(".isEmptyWarning")) | ||
| } | ||
| if (is.null(getGeneric("metaData"))) { | ||
| setGeneric("metaData", function(object) standardGeneric("metaData")) | ||
| } | ||
| if (is.null(getGeneric("metaData<-"))) { | ||
| setGeneric("metaData<-", | ||
| function(object, value) standardGeneric("metaData<-")) | ||
| } | ||
| if (is.null(getGeneric("coordinates"))) { | ||
| setGeneric("coordinates", | ||
| function(object, ...) standardGeneric("coordinates")) | ||
| } | ||
| if (is.null(getGeneric("coordinates<-"))) { | ||
| setGeneric("coordinates<-", | ||
| function(object, value) standardGeneric("coordinates<-")) | ||
| } | ||
| setGeneric("mz", function(object, ...) standardGeneric("mz")) | ||
| setGeneric("mz<-", function(object, value) standardGeneric("mz<-")) | ||
|
|
||
| setGeneric("intensity", function(object, ...) standardGeneric("intensity")) | ||
| setGeneric( | ||
| "intensity<-", | ||
| function(object, value) standardGeneric("intensity<-") | ||
| ) | ||
| setGeneric("isEmpty", function(x) standardGeneric("isEmpty")) | ||
| setGeneric(".isEmptyWarning", function(x) standardGeneric(".isEmptyWarning")) | ||
| setGeneric("metaData", function(object) standardGeneric("metaData")) | ||
| setGeneric("metaData<-", function(object, value) standardGeneric("metaData<-")) | ||
| setGeneric("coordinates", function(object, ...) standardGeneric("coordinates")) | ||
| setGeneric( | ||
| "coordinates<-", | ||
| function(object, value) standardGeneric("coordinates<-") | ||
| ) | ||
| ## end of AbstractMassObject | ||
|
|
||
| ## MassSpectrum | ||
| if (is.null(getGeneric("calibrateIntensity"))) { | ||
| setGeneric("calibrateIntensity", | ||
| function(object, ...) standardGeneric("calibrateIntensity")) | ||
| } | ||
| if (is.null(getGeneric("detectPeaks"))) { | ||
| setGeneric("detectPeaks", | ||
| function(object, ...) standardGeneric("detectPeaks")) | ||
| } | ||
| if (is.null(getGeneric("estimateBaseline"))) { | ||
| setGeneric("estimateBaseline", | ||
| function(object, method=c("SNIP", "ConvexHull", "Median"), ...) | ||
| standardGeneric("estimateBaseline")) | ||
| } | ||
| if (is.null(getGeneric("estimateNoise"))) { | ||
| setGeneric("estimateNoise", | ||
| function(object, ...) standardGeneric("estimateNoise")) | ||
| } | ||
| if (is.null(getGeneric(".findLocalMaxima"))) { | ||
| setGeneric(".findLocalMaxima", | ||
| function(object, halfWindowSize=20L) | ||
| standardGeneric(".findLocalMaxima")) | ||
| } | ||
| if (is.null(getGeneric(".findLocalMaximaLogical"))) { | ||
| setGeneric(".findLocalMaximaLogical", | ||
| function(object, halfWindowSize=20L) | ||
| standardGeneric(".findLocalMaximaLogical")) | ||
| } | ||
| if (is.null(getGeneric("isRegular"))) { | ||
| setGeneric("isRegular", | ||
| function(object, ...) standardGeneric("isRegular")) | ||
| } | ||
| if (is.null(getGeneric("removeBaseline"))) { | ||
| setGeneric("removeBaseline", | ||
| function(object, ...) standardGeneric("removeBaseline")) | ||
| } | ||
| if (is.null(getGeneric("smoothIntensity"))) { | ||
| setGeneric("smoothIntensity", | ||
| function(object, ...) | ||
| standardGeneric("smoothIntensity")) | ||
| } | ||
| if (is.null(getGeneric("totalIonCurrent"))) { | ||
| setGeneric("totalIonCurrent", | ||
| function(object) standardGeneric("totalIonCurrent")) | ||
| } | ||
| setGeneric( | ||
| "calibrateIntensity", | ||
| function(object, ...) standardGeneric("calibrateIntensity") | ||
| ) | ||
| setGeneric("detectPeaks", function(object, ...) standardGeneric("detectPeaks")) | ||
| setGeneric( | ||
| "estimateBaseline", | ||
| function(object, method=c("SNIP", "ConvexHull", "Median"), ...) | ||
| standardGeneric("estimateBaseline")) | ||
| setGeneric( | ||
| "estimateNoise", function(object, ...) standardGeneric("estimateNoise") | ||
| ) | ||
| setGeneric( | ||
| ".findLocalMaxima", | ||
| function(object, halfWindowSize=20L) standardGeneric(".findLocalMaxima") | ||
| ) | ||
| setGeneric( | ||
| ".findLocalMaximaLogical", | ||
| function(object, halfWindowSize=20L) | ||
| standardGeneric(".findLocalMaximaLogical") | ||
| ) | ||
| setGeneric("isRegular", function(object, ...) standardGeneric("isRegular")) | ||
| setGeneric( | ||
| "removeBaseline", function(object, ...) standardGeneric("removeBaseline") | ||
| ) | ||
| setGeneric( | ||
| "smoothIntensity", function(object, ...) standardGeneric("smoothIntensity") | ||
| ) | ||
| setGeneric( | ||
| "totalIonCurrent", function(object) standardGeneric("totalIonCurrent") | ||
| ) | ||
| ## end of MassSpectrum | ||
|
|
||
| ## MassPeaks | ||
| if (is.null(getGeneric("labelPeaks"))) { | ||
| setGeneric("labelPeaks", function(object, ...) standardGeneric("labelPeaks")) | ||
| } | ||
| if (is.null(getGeneric("monoisotopicPeaks"))) { | ||
| setGeneric("monoisotopicPeaks", | ||
| function(object, ...) standardGeneric("monoisotopicPeaks")) | ||
| } | ||
| if (is.null(getGeneric("snr"))) { | ||
| setGeneric("snr", function(object) standardGeneric("snr")) | ||
| } | ||
| setGeneric("labelPeaks", function(object, ...) standardGeneric("labelPeaks")) | ||
| setGeneric( | ||
| "monoisotopicPeaks", | ||
| function(object, ...) standardGeneric("monoisotopicPeaks") | ||
| ) | ||
| setGeneric("snr", function(object) standardGeneric("snr")) | ||
| ## end of MassPeaks |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| ## .as.occurrence.list | ||
| ## internal function to create a list of peaks occurrence | ||
| ## | ||
| ## params: | ||
| ## l: list of AbstractMassObject objects | ||
| ## | ||
| ## returns: | ||
| ## a list, where sample is the sample id, i is the index of the uniqueMass, | ||
| ## and mass is the unique mass vector | ||
| .as.occurrence.list.MassObjectList <- function(l) { | ||
| .stopIfNotIsMassObjectList(l) | ||
|
|
||
| mass <- .unlist(lapply(l, function(x)x@mass)) | ||
| uniqueMass <- sort.int(unique(mass)) | ||
| n <- lengths(l) | ||
|
|
||
| list( | ||
| sample = rep.int(seq_along(l), lengths(l)), | ||
| i = findInterval(mass, uniqueMass), | ||
| mass = uniqueMass | ||
| ) | ||
| } |
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