Quantitative Analysis of Mass Spectrometry Data

A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.


News

RELEASE HISTORY OF THE "MALDIquant" PACKAGE

CHANGES IN MALDIquant VERSION 1.19.2 [2019-05-12]:

BUGFIXES

  • approxfun: remove wrong generic. Thanks to Martin Mächler for reporting.
  • Remove useless generics for as.matrix, length, lines, points, plot.

CHANGES IN MALDIquant VERSION 1.19.2 [2019-03-13]:

BUGFIXES

  • binPeaks propagated values to empty MassPeaks objects; see #61. Thanks to Chase Clark (@chasemc) for reporting.

CHANGES IN MALDIquant VERSION 1.19.1 [2019-03-03]:

BUGFIXES

  • calibratyIntensity ignored the mc.cores argument. Thanks to @dsammour for reporting.

CHANGES IN MALDIquant VERSION 1.19 [2018-11-26]:

IMPROVEMENTS:

  • determineWarpingFunctions's return value gains a new argument nmatch storing the number of matches of the given peaks against the reference; see #59. Suggested by Melanie Föll (@foellmelanie).

CHANGES IN MALDIquant VERSION 1.18.1 [2018-10-04]:

INTERNAL CHANGES

  • determineWarpingFunctions, change handling of minimal necessary peaks for each warping method.

CHANGES IN MALDIquant VERSION 1.18 [2018-07-06]:

IMPROVEMENTS

  • determineWarpingFunctions gains an allowNoMatches argument. If allowNoMatches is TRUE a warning is thrown instead of an error and the resulting list of warping functions will contain NA at the specific index; see #57. Suggested by Melanie Föll (@foellmelanie).
  • warpMassPeaks/warpMassSpectra gain an emptyNoMatches argument. If emptyNoMatches is TRUE the intensity values of MassPeaks/MassSpectra objects with missing warping functions are set to zero; see #57 for details. Suggested by Melanie Föll (@foellmelanie).
  • alignSpectra gain two new arguments: allowNoMatches and emptyNoMatches; see #57 for details. Suggested by Melanie Föll (@foellmelanie).
  • The manual pages of alingSpectra, binPeaks, determineWarpingFunctions and referencePeaks gain a sentence for use of the "tolerance" argument in ppm; see issue #56 for details; Suggested by Jimmy Lawrence [email protected].

REMOVED ARGUMENT

  • plot now doesn't draw a horizontal line at y == 0 anymore. The argument "abline.col" was removed as well. To get the old behaviour call plot(spectrum); abline(h=0, col="#808080"); Suggested by Jimmy Lawrence [email protected].

CHANGES IN MALDIquant VERSION 1.17 [2017-11-12]:

NEW FEATURES

  • smoothIntensity gains a new argument "weighted" (default: FALSE) for method="MovingAverage". If TRUE a weighted moving average is applied. Added by Sigurdur Smarason.

CHANGES IN MALDIquant VERSION 1.16.4 [2017-08-27]:

BUGFIXES

  • coordinates now returns NULL (instead of an error) if there are no imaging information in the metadata of a spectrum/peaks list.

CHANGES IN MALDIquant VERSION 1.16.3 [2017-05-30]:

IMPROVEMENTS

  • Mass values are sorted now if they were not before; affected functions: createMassSpectrum, createMassPeaks, validObject.

INTERNAL

  • Replace sort.int(..., method="quick") by sort.int(...) and let R decide which sorting method is appropriated ("radix"/"insert" [default] is often faster than "quick").

CHANGES IN MALDIquant VERSION 1.16.2 [2017-04-04]:

INTERNAL

  • Disable symbol search for native C routines.

CHANGES IN MALDIquant VERSION 1.16.1 [2016-12-23]:

BUGFIXES

  • match.closest: fix results for x >= max(table).

CHANGES IN MALDIquant VERSION 1.16 [2016-12-13]:

NEW FEATURES

  • match.closest allows relaxed matching.

INTERNAL

  • The former hidden .which.closest is renamed into the exported match.closest and gains a "tolerance" and "nomatch" argument to allow relaxed matching.
  • .pseudoCluster use the new match.closest (could result in slightly different tolerance values).

CHANGES IN MALDIquant VERSION 1.15 [2016-06-25]:

NEW FEATURES

  • Add monoisotopicPeaks to find monoisotopic peaks in MassPeaks objects.

IMPROVEMENTS

  • plot: x-axis label is "m/z" now (was "mass" before). Thanks to Robert Winkler [email protected] for reporting of the sometimes misleading label.
  • Add mz and mz<- (same as mass/mass<-) to follow ProtGenerics guidelines and for consistency.

BUGFIXES

  • labelPeaks didn't respect "srt=c(90, 180, 270, 360)" if "avoidOverlap=TRUE". Please note that "srt %% 90 != 0" in combination with "avoidOverlap=TRUE" is still not supported!

INTERNAL

  • Throw a warning if plotMsiSlice was called on a interactive device with multiple centers (the warning was not thrown correctly before).
  • Throw an error if trim,list was called on a generic list instead of a list of AbstractMassObjects.
  • Remove textLabelRect-functions.R and move its content to calculateLabelPositions-functions.R.

CHANGES IN MALDIquant VERSION 1.14 [2015-11-18]:

IMPROVEMENTS

  • ?estimateBaseline: clarify that "decreasing=TRUE" is the default for the SNIP baseline estimation algorithm (estimateBaseline(..., method="SNIP")).

BUGFIXES

  • MALDIquant depends on R 3.2.0 now. Due to a bug in R (PR#15707, fixed in R 3.2.0) the ... argument was not interpreted in nested function calls. This results in failures of calibratyIntensity on R < 3.2.0.

REMOVED ARGUMENTS/FUNCTIONS

  • plotImsSlice: (was defunct since 1.13) use plotMsiSlice instead. It has slightly different arguments; see ?plotMsiSlice for details.

INTERNAL CHANGES:

  • .as.binary.matrix now always returns an integer matrix.

CHANGES IN MALDIquant VERSION 1.13 [2015-09-16]:

IMPROVEMENTS

  • calibratyIntensity gains a "range" argument for "median" and "PQN" as well; in 1.12 just "TIC" was supported.
  • Extend example section in ?MALDIquant-parallel manual page.
  • Add hint about relative tolerance in manual pages ?alignSpectra, ?binPeaks, ?determineWarpingFunctions and ?referencePeaks; Thanks to Damien Portevin [email protected] for reporting of the ambiguous phrase.

MODIFICATIONS

  • Rewrite DESCRIPTION and explain acronyms to follow the latest version of the CRAN Repository Policy.

DEFUNCT ARGUMENTS/FUNCTIONS

  • plotImsSlice: use plotMsiSlice instead. It has slightly different arguments; see ?plotMsiSlice for details.

BUGFIXES

  • calibrateIntensity: don't apply a scaling factor that equals zero anymore (happens in rare cases for method="median"). It throws a warning instead and leaves the spectrum untouched; fixes #51.
  • .plotMsiSlice just used the first center if "combine=TRUE"; affected functions: plotMsiSlice.
  • Add smoothIntensity to the ?MALDIquant-parallel manual page. Thanks to Leiming Yu [email protected] for reporting the missing entry.

INTERNAL CHANGES

  • Importing non-base functions/methods from recommended R packages (graphics, stats, ...) as required by R-devel.
  • Turn .calculateLabelPositions, .testLabelOverlap, .labelOverlap into normal functions (were methods before).
  • msiSlices: use NA_real_ instead of logical NA.

CHANGES IN MALDIquant VERSION 1.12 [2015-06-11]:

NEW FEATURES

  • Add as for MassPeaks to convert them into MassSpectrum objects.
  • Add coordinates methods for AbstractMassObjects and list objects to access/set coordinates for MSI datasets.
  • Add msiSlices functions to create slices of a MSI dataset.
  • calibratyIntensity(object, method="TIC"): gains a "range" argument allowing to calibrate spectra by TIC on a specific mass range; closes #27.
  • Add parallel support on unix-based platforms using the parallel package. The following functions/methods supports the "mc.cores" argument (default is 1): trim, transformIntensity, removeBaseline, calibrateIntensity, detectPeaks, alignSpectra, averageMassSpectra, mergeMassPeaks; Please read also ?"MALDIquant-parallel".

IMPROVEMENTS

  • intensityMatrix: rewrite to improve execution time.
  • trim: rewrite to improve execution time.

MODIFICATIONS

  • Change generics of mass and intensity from function(object) to function(object, ...) to provide the same generics as Bioconductor's ProtGenerics package.
  • intensityMatrix: gains an attribute "mass" that stores the unique mass.

DEPRECATED ARGUMENTS/FUNCTIONS

  • plotImsSlice: use plotMsiSlice instead. It has slightly different arguments; see ?plotMsiSlice for details.

REMOVED ARGUMENTS/FUNCTIONS

  • intensityMatrix for MassSpectrum objects (was defunct since 1.10).

BUGFIXES

  • Fix vignette call in ?MALDIquant-package.

INTERNAL CHANGES

  • The return value of the internal .as.matrix.MassObjectList function gains an attribute "mass" that stores the unique mass (conversions of the colnames are not needed anymore); affected functions: intensityMatrix
  • Remove some useless cbind calls in .estimateNoise* and .estimateBaseline; no user visible changes; affected functions: estimateNoise, estimateBaseline, detectPeaks
  • Remove superfluous arguments in internal .calibrateIntensitySimple.
  • Avoid double check for negative intensity values in transformIntensity.

CHANGES IN MALDIquant VERSION 1.11 [2014-08-11]:

NEW FEATURES

  • Add plotImsSlice: a function to plot Imaging Mass Spectrometry data.

MODIFICATIONS

  • Rename the vignette to MALDIquant-intro.pdf.
  • Move the content of the manual pages of .savitzkyGolay and .movingAverage to smoothIntensity and remove the old ones.
  • Move the content of the manual pages of .estimateBaseline{Snip,TopHat,ConvexHull,Median} to estimateBaseline and remove the old ones.
  • Move the content of the manual pages of .estimateNoise{Mad,SuperSmoother} to estimateNoise and remove the old ones.

CHANGES IN MALDIquant VERSION 1.10 [2014-04-11]:

IMPROVEMENTS

  • Add a general vignette.
  • createMassSpectrum/createMassPeaks: a warning is shown if negative intensity values are found.
  • .transformIntensity: a warning is shown if negative intensity values are generated and set them to zero; affected functions: transformIntensity, smoothIntensity, calibrateIntensity.
  • determineWarpingFunctions: a warning is shown if the "reference" contains less than ten peaks; affected functions: determineWarpingFunctions, alignSpectra
  • trim: a warning is shown if the resulting MassSpectrum/MassPeaks object does not contain any data points.

MODIFICATIONS

  • Use table instead of any(length(fiedler2009subset[[1]]) == sapply(... in demo/workflow.R.

DEFUNCT ARGUMENTS/FUNCTIONS

  • intensityMatrix for MassSpectrum objects.

REMOVED ARGUMENTS/FUNCTIONS

  • isMassObject/isMassObjectList: use isMassSpectrum, isMassPeaks, isMassSpectrumList or isMassPeaksList instead.
  • totalIonCurrent,MassPeaks-method: TIC of peaks is meaningless.
  • totalIonCurrent<-,MassSpectrum-method: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • standardizeTotalIonCurrent: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • calibrate: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • ltrim/rtrim: use trim(..., range=c(min, max)) instead.
  • determineWarpingFunctions, argument "warpingFunction": use "method" argument instead.
  • mergeMassPeaks, argument "fun": use "method" argument instead.
  • mergeMassSpectra: use averageMassSpectra.
  • savitzkyGolay: use smoothIntensity(..., method="SavitzkyGolay") instead.
  • movingAverage: use smoothIntensity(..., method="MovingAverage") instead.
  • transformIntensity, argument "fun": use "method" argument instead.
  • removeBaseline, argument "fun": use "method" argument instead.
  • detectPeaks, argument "fun": use "method" argument instead.

BUGFIXES

  • .which.closest: check limits to avoid missing matches in some rare edge cases; affected functions: labelPeaks.
  • Add missing reference "Andrew 1979" to the .estimateBaselineConvexHull manual page.

INTERNAL CHANGES

  • estimateNoise: move body of estimateNoise,MassSpectrum to internal .estimateNoise.
  • Move tests into tests/testthat/ to adapt to testthat 0.8 and new CRAN policy; closes #44.
  • .localMaximaR: removed. It was replaced by a C version of .localMaxima in 1.5.
  • .snipR: removed. It was replaced by a C version of .estimateBaselineSnip in 0.2.
  • .lowerConvexHullR: removed. It was replaced by a C version of .estimateBaselineConvexHull in 0.3.
  • .topHatR: removed. It was never used and replaced by a C version of .estimateBaselineTopHat in 1.6.

CHANGES IN MALDIquant VERSION 1.9 [2014-01-14]:

NEW FEATURES

  • Add alignSpectra: a wrapper around detectPeaks, determineWarpingFunctions and warpMassSpectra to provide an easier workflow.

IMPROVEMENTS

  • filterPeaks: introduce "mergeWhitelists" argument to additionally keep peaks that occur at least in one group. The default behaviour does not changed. Please see the man page of filterPeaks for details.
  • intensityMatrix: add "spectra" argument to allow interpolation of missing peaks if corresponding spectra is given.
  • Replace some lapply calls by mapply to allow different "halfWindowSize" arguments etc.; affected methods: smoothIntensity, removeBaseline, detectPeaks.

MODIFICATIONS

  • filterPeaks: "minFrequency" > 1 and "minNumber" > n is not set to 1 or n anymore; only a warning about "empty peak whitelists" is given; see also issue #26.
  • filterPeaks: replace warning about too large "minFrequency" or "minNumber" by a warning about "empty peak whitelists".
  • intensityMatrix: rename first argument to "peaks"
  • demo/workflow.R: introduce alignSpectra.
  • demo/warping.R: adapt to current preferred workflow.
  • demo/peaks.R: add smoothing and a few new plots.

DEPRECATED ARGUMENTS/FUNCTIONS

  • intensityMatrix for MassSpectrum objects.

DEFUNCT ARGUMENTS/FUNCTIONS

  • isMassObject/isMassObjectList: use isMassSpectrum, isMassPeaks, isMassSpectrumList or isMassPeaksList instead.
  • totalIonCurrent,MassPeaks-method: TIC of peaks is meaningless.
  • totalIonCurrent<-,MassSpectrum-method: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • standardizeTotalIonCurrent: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • calibrate: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • ltrim/rtrim: use trim(..., range=c(min, max)) instead.
  • determineWarpingFunctions, argument "warpingFunction": use "method" argument instead.
  • mergeMassPeaks, argument "fun": use "method" argument instead.
  • mergeMassSpectra: use averageMassSpectra.
  • savitzkyGolay: use smoothIntensity(..., method="SavitzkyGolay") instead.
  • movingAverage: use smoothIntensity(..., method="MovingAverage") instead.
  • transformIntensity, argument "fun": use "method" argument instead.
  • removeBaseline, argument "fun": use "method" argument instead.
  • detectPeaks, argument "fun": use "method" argument instead.

BUGFIXES

  • plot: fix subtitle for averaged spectra.

INTERNAL CHANGES

  • Add .as.matrix.MassObjectList to avoid internal dependencies on intensityMatrix; affected functions: filterPeaks, referencePeaks.
  • Add .as.binary.matrix.
  • Remove man/MALDIquant-internal.Rd.
  • Argument "representation" of setClass is deprecated since R 3.0.0; use "slots" instead. affected classes: AbstractMassObject, MassPeaks, MassSpectrum.

CHANGES IN MALDIquant VERSION 1.8 [2013-09-08]:

NEW FEATURES

  • Add smoothIntensity: to apply smoothing filters. Supports "SavitzkyGolay" and "MovingAverage". savitzkyGolay and movingAverage are now marked as deprecated.
  • Add calibrateIntensity: to calibrate/normalize intensity values. Supports "TIC", "median" and "PQN" calibration/normalization. It replaces three similar functions with different names: totalIonCurrent<-, standardizeTotalIonCurrent, calibrate (these three are marked as deprecated and will be removed in future releases).
  • Add averageMassSpectra: supports "mean", "median" and "sum" aggregation of spectra. It replaces mergeMassSpectra.
  • Add C implementation of colMedians for faster averaging/merging of MassSpectrum/MassPeaks objects.
  • Add LongVector support; now MALDIquant depends on R >= 3.0.0.

MODIFICATIONS

  • MassSpectrum/MassPeaks class: change representation of slots mass, intensity, snr to "numeric" (was "vector" before). Should not affect anything. Maybe you have to reimport raw data and resave RData files.
  • trim: replace "minMass" and "maxMass" arguments by new "range" argument.
  • transformIntensity: add "method" argument (supports "sqrt", "log", "log2", "log10"). "fun" argument is deprecated.
  • estimateBaseline/removeBaseline: rename argument method="Median" to method="median".
  • determineWarpingFunctions: add "method" argument (supports "lowess", "linear", "quadratic", "cubic"); "warpingFunctions" argument is deprecated.
  • mergeMassPeaks: add "method" (supports "mean", "median", "sum") argument; "fun" argument is deprecated.

DEPRECATED ARGUMENTS/FUNCTIONS

  • isMassObject/isMassObjectList: use isMassSpectrum, isMassPeaks, isMassSpectrumList or isMassPeaksList instead.
  • totalIonCurrent,MassPeaks-method: TIC of peaks is meaningless.
  • totalIonCurrent<-,MassSpectrum-method: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • standardizeTotalIonCurrent: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • calibrate: use calibrateIntensity(..., method="TIC") instead to calibrate/normalize MassSpectrum objects.
  • ltrim/rtrim: use trim(..., range=c(min, max)) instead.
  • determineWarpingFunctions, argument "warpingFunction": use "method" argument instead.
  • mergeMassPeaks, argument "fun": use "method" argument instead.
  • mergeMassSpectra: use averageMassSpectra.
  • savitzkyGolay: use smoothIntensity(..., method="SavitzkyGolay") instead.
  • movingAverage: use smoothIntensity(..., method="MovingAverage") instead.
  • transformIntensity, argument "fun": use "method" argument instead.
  • removeBaseline, argument "fun": use "method" argument instead.
  • detectPeaks, argument "fun": use "method" argument instead.

REMOVED FUNCTIONS

  • iplot: because it throws NOTEs on CRAN's R CMD check and the most important function grDevices::getGraphicEvents behaves different on Unix/Windows platform (some keys don't working) and contains some nasty bugs, e.g.: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15208 Also the "zoom" R package provides similar functionality.

BUGFIXES

  • totalIonCurrent: fix calculation by estimating the integral; fixes #29. affected functions: totalIonCurrent, calibrateIntensity(..., method="TIC").
  • filterPeaks: reduce minNumber to length(l) to avoid complete removal of peaks; fixes #26.
  • src/snip.c: fix some segmention faults because of a missing PROTECT for "duplicate" call. affected functions: estimateBasline/removeBaseline(..., method="SNIP")
  • Add import("methods") to NAMESPACE (fixes #36).

INTERNAL CHANGES

  • Remove internal imputeMass.
  • Remove internal .replaceNonEmptyMassObjects.
  • approxfun: returns NA for empty MassSpectrum objects.
  • [ (subset method): little speed up by calling which to evaluate logical expressions only once.
  • Use integer values where possible.
  • Modify C written functions to support LongVectors; closes #13; now MALDIquant depends on R >= 3.0.0.

CHANGES IN MALDIquant VERSION 1.7 [2013-05-23]:

NEW FEATURES

  • Add isRegular method to test MassSpectrum objects for regular increasing mass values/intervals; closes #23.
  • Add savitzkyGolay, Savitzky-Golay Smoothing Filter.
  • Add memory usage to show output.
  • iplot: add horizontal distance measurement (using left mouse clicks).
  • filterPeaks: add "minNumber" argument to allow an absolute threshold for filtering; closes #21.
  • demo/workflow.R: add raw data check.

IMPROVEMENTS

  • demo/workflow.R: replace moving average smoother by Savitzky-Golay-Filter.
  • .estimateBaselineSnip: support decreasing/increasing clipping window; controlled by new argument "decreasing"; use a decreasing window per default to get a smoother baseline; (use decreasing=FALSE to get the old behaviour).
  • isEmpty: treat spectra with only zeros as intensity values as empty ones.
  • movingAverage: left/right extrema now calculated for 0:windowSize and (n-windowSize+1):n (before they were set to NA).

BUGFIXES

  • filterPeaks: doesn't round (floor) minFrequency argument anymore; led to unexpected results; fixes #22.
  • mergeMassSpectra: empty MassSpectrum objects are ignored now (but if all objects are empty mergeMassSpectra will return an empty MassSpectrum object, too); fixes #20.
  • .mergeMetaData: fix merging of lists with different lengths; fixes #17. affected functions: mergeMassPeaks, mergeMassSpectra.
  • .doByLabels: preserve order of non-factor labels; fixes #19; affected functions:filterPeaks,mergeMassPeaks,mergeMassSpectra`.
  • totalIonCurrent/isEmpty: fix integer overflow; fixes #25.
  • totalIonCurrent<-: fix handling of empty spectra; fixes #15.
  • Remove LICENSE file.

INTERNAL CHANGES

  • Replace all paste(..., sep="") calls by paste0; now MALDIquant depends on R >= 2.15.
  • Replace all .C interfaces by .Call.

CHANGES IN MALDIquant VERSION 1.6 [2013-03-01]:

NEW FEATURES

  • Add interactive plot method: iplot.
  • Add TopHat baseline estimation: estimateBaseline(..., method="TopHat")/ removeBaseline(..., method="TopHat").

IMPROVEMENTS

  • Include tests in inst/tests.

BUGFIXES

  • .which.closest: rounding .5 to the next highest integer (before: to the next lowest one); affected functions: labelPeaks.
  • .doByLabels: fix an error that occurred if all labels were unique (fixes #1); affected functions: filterPeaks, mergeMassPeaks, mergeMassSpectra.
  • estimateBaseline(..., method="Median"): do not allow a window size > n (fixes #4).

CHANGES IN MALDIquant VERSION 1.5 [2012-12-06]:

NEW FEATURES

  • Add movingAverage.
  • labelPeaks: add labels argument.

IMPROVEMENTS

  • detectPeaks: only throw an error if windowSize > length (windowSize == length is no error anymore).
  • .doByLabels: drop unused levels of argument "labels"; affected functions: filterPeaks, mergeMassPeaks, mergeMassSpectra.
  • Rewrite localMaxima in C to reduce running time and memory consumption.

CHANGES IN MALDIquant VERSION 1.4 [2012-10-30]:

NEW FEATURES

  • Add slot "snr" to MassPeaks.
  • Add .estimateNoiseMad (same implementation as old estimateNoise method).
  • Add .estimateNoiseSuperSmoother.
  • estimateNoise: add method argument, change return value to two column matrix.
  • binPeaks/referencePeaks: add argument method=c("strict", "relaxed"); "relaxed" allows multiple peaks of the same spectrum in a bin.

IMPROVEMENTS

  • labelPeaks: remove tolerance argument (now always select the closest one).
  • mergeMassPeaks/mergeMassSpectra: merge metaData, too.
  • detectPeaks: new example for a custom noise estimation function.
  • calibrate: add ... to generic definition of calibrate.
  • Change demo licences to public domain.

INTERNAL CHANGES

  • detectPeaks: change internal snr handling.
  • show: rewrite (OO design).

CHANGES IN MALDIquant VERSION 1.3 [2012-09-16]:

NEW FEATURES

  • Add trim and [ methods.
  • labelPeaks: add avoidOverlap argument to avoid overlapping of peak labels.

IMPROVEMENTS

  • detectPeaks: add error message if windowSize >= length.
  • determineWarpingFunctions: add error message if it could not match any peak to reference peaks.

MODIFICATIONS

  • labelPeaks: change default value for verticalOffset argument.
  • labelPeaks: remove family argument.

BUGFIXES

  • Fix isMassSpectrumList.

GENERAL

  • Update DESCRIPTION file to use [email protected] and depends on R>=2.14 now.
  • Add CITATION file.

CHANGES IN MALDIquant VERSION 1.2 [2012-07-18]:

BUG FIXES

  • determineWarpingFunctions: stop with an error if reference MassPeaks object is empty.
  • .doByLabel: preserve list order (affects filterPeaks).

INTERNAL CHANGES

  • Replace some sapply calls by lapply.

CHANGES IN MALDIquant VERSION 1.1 [2012-05-06]:

NEW FEATURES

  • Add totalIonCurrent method (replacement for calibrate function on MassSpectrum objects).
  • Add methods accepting lists as arguments: transformIntensity, removeBaseline, detectPeaks.

MODIFICATIONS

  • detectPeaks: remove localMaxima argument.
  • detectPeaks: replace noise argument by fun.
  • removeBaseline: replace baseline argument by fun.
  • labelPeaks: use par("usr") to calculate default verticalOffset.
  • labelPeaks: add absoluteVerticalPos argument.
  • plot: change "sub" for merged spectra/peaks.
  • intensityMatrix: remove argument replaceByNa.
  • determineWarpingFunctions, warpMassSpectra, warpMassPeaks now require lists as arguments and return a list.
  • calibrate: works only on matrices now.
  • Replace all lapply calls by new methods in demonstration scripts.
  • Allow only numeric values for intensity<- and mass<-.
  • Rename findLocalMaxima to .findLocalMaxima and hide by NAMESPACE.
  • Rename dataset spectra in fiedler2009subset.
  • Remove peaks dataset.

CHANGES IN MALDIquant VERSION 1.0 [2012-03-28]:

NEW FEATURES

  • Add demonstration scripts.
  • Add functions: binPeaks, determineWarpingFunctions, filterPeaks, isMassObject, isMassPeaks, isMassSpectrum, mergeMassPeaks, mergeMassSpectra, referencePeaks, warpMassPeaks, warpMassSpectra.

MODIFICATIONS

  • Change NAMESPACE.
  • Hide imputeMass method because it fails on Bruker Daltonics' CompassXport 32bit output.
  • Add \keyword{internal} to estimateBasline*-functions.Rd.
  • labelPeaks: rename massTolerance argument to tolerance.
  • Replace dataset sA1/pA1 by spectra/peaks (containing 16 example spectra).

CHANGES IN MALDIquant VERSION 0.5 [2012-01-18]:

NEW FEATURES

  • Add imputeMass method.

IMPROVEMENTS

  • Rewrite intensityMatrix function (little speed improvement).

CHANGES IN MALDIquant VERSION 0.4 [2011-08-04]:

NEW FEATURES

  • Add functions: isMassObjectList, isMassPeaksList, isMassSpectrumList, findEmptyMassObjects, removeEmptyMassObjects, intensityMatrix and calibrate (only TIC supported up to now).
  • Add mass and massTolerance argument to labelPeaks.

IMPROVEMENTS

  • Change default value for verticalOffset argument in labelPeaks.
  • Add pA1 dataset.

MODIFICATIONS

  • Rename AbstractMassSpectrumData to AbstractMassObject.

CHANGES IN MALDIquant VERSION 0.3 [2011-05-28]:

NEW FEATURES

  • Add transformIntensity, estimateNoise, findLocalMaxima, detectPeaks and points method.
  • Add createMassPeaks constructor.

IMPROVEMENTS

  • Replace .estimateBaselineMovingEstimator by .estimateBaselineMedian (uses runmed instead of an own slow movingEstimator function).

MODIFICATIONS

  • Rewrite labelPeaks (some arguments changed).
  • Rename SingleSpectrum class to MassSpectrum.
  • Rename SinglePeakList class to MassPeaks.
  • Remove fdrtool dependency and rewrite .estimateBaselineConvexHull in C.
  • Move importing functions to the following R-packages: readBrukerFlexData, readMzXmlData.

BUGFIXES

  • change .C(..., DUP=F) to .C(..., DUP=T) in .estimateBaselineSnip to avoid changes of global variables.

CHANGES IN MALDIquant VERSION 0.2 [2011-03-29]:

  • Add baseline correction algorithm SNIP (implemented in C) [default].
  • Add MovingEstimator and ConvexHull baseline estimation algorithm.
  • Add as.matrix, intensity, length, lines, mass and metaData methods.
  • Add basic SinglePeakList class, adopt plot and lines, add labelPeaks (still useless).

CHANGES IN MALDIquant VERSION 0.1 [2011-02-22]:

  • First public release.
  • Up to now only importing and plotting of a single mass spectrum are supported.

Reference manual

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install.packages("MALDIquant")

1.19.3 by Sebastian Gibb, 5 months ago


http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquant/


Report a bug at https://github.com/sgibb/MALDIquant/issues/


Browse source code at https://github.com/cran/MALDIquant


Authors: Sebastian Gibb [aut, cre] , Korbinian Strimmer [ths]


Documentation:   PDF Manual  


Task views: Chemometrics and Computational Physics


GPL (>= 3) license


Imports parallel

Depends on methods

Suggests knitr, testthat


Depended on by MALDIquantForeign, MALDIrppa.


See at CRAN