Man pages for sneumann/xcms-presvnbridge
LC/MS and GC/MS Data Analysis

absent-methodsDetermine which peaks are absent / present in a sample class
AutoLockMass-methodsAutomatic parameter for Lock mass fixing 'AutoLockMass' ~~
calibrateCalibrate peaks for correcting unprecise m/z values
collect-methodsCollect MS^n peaks into xcmsFragments
colMaxFind row and column maximum values
c.xcmsSetCombine xcmsSet objects
descendZeroFind start and end points of a peak
diffreport-methodsCreate report of analyte differences
doubleMatrixAllocate double, integer, or logical matricies
etgEmpirically Transformed Gaussian function
fillPeaks.chrom-methodsIntegrate areas of missing peaks
fillPeaks-methodsIntegrate areas of missing peaks
fillPeaks.MSW-methodsIntegrate areas of missing peaks in FTICR-MS data
filtfftApply an convolution filter using an FFT
findEqualGreaterFind values in sorted vectors
findMZFind fragment ions in xcmsFragment objects
findneutralFind neutral losses in xcmsFragment objects
findPeaks.centWave-methodsFeature detection for high resolution LC/MS data
findPeaks.massifquant-methodsFeature detection for high resolution LC/MS data
findPeaks.matchedFilter-methodsFeature detection in the chromatographic time domain
findPeaks-methodsFeature detection for GC/MS and LC/MS Data - methods
findPeaks.MS1-methodsCollecting MS1 precursor peaks
findPeaks.MSW-methodsFeature detection for single-spectrum non-chromatography MS...
getEIC-methodsGet extracted ion chromatograms for specified m/z ranges
getPeaks-methodsGet peak intensities for specified regions
getScan-methodsGet m/z and intensity values for a single mass scan
getSpec-methodsGet average m/z and intensity values for multiple mass scans
group.densityGroup peaks from different samples together
group-methodsGroup peaks from different samples together
group.mzClustGroup Peaks via High Resolution Alignment
groupnames-methodsGenerate unque names for peak groups
group.nearestGroup peaks from different samples together
groupval-methodsExtract a matrix of peak values for each group
image.xcmsRawPlot log intensity image of a xcmsRaw object
loadRaw-methodsRead binary data from a source
medianFilterApply a median filter to a matrix
msn2xcmsRawCopy MSn data in an xcmsRaw to the MS slots
na.flatfillFill in NA values at the extremes of a vector
netCDFHigh-performance, low-level access to NetCDF data files
netCdfSource-classClass '"netCdfSource"', for reading raw data from 'netCDF'...
panel.corCorrelation coefficient panel for pairs function
peakPlots-methodsPlot a grid of a large number of peaks
peakTable-methodsCreate report of aligned peak intensities
plotChrom-methodsPlot extracted ion chromatograms from the profile matrix
plotEIC-methodsPlot extracted ion chromatograms for specified m/z range
plotPeaks-methodsPlot a grid of a large number of peaks
plotRaw-methodsScatterplot of raw data points
plotrt-methodsPlot retention time deviation profiles
plotScan-methodsPlot a single mass scan
plotSpec-methodsPlot mass spectra from the profile matrix
plotSurf-methodsPlot profile matrix 3D surface using OpenGL
plotTIC-methodsPlot total ion count
plot.xcmsEICPlot extracted ion chromatograms from multiple files
profGenerateGeneration of profile data
profMedFilt-methodsMedian filtering of the profile matrix
profMethod-methodsGet and set method for generating profile data
profRange-methodsSpecify a subset of profile mode data
profStep-methodsGet and set m/z step for generating profile data
pvalGenerate p-values for a vector of t-statistics
rampHigh-performance, low-level access to mzXML/mzData files
rampSource-classClass '"rampSource"', for reading raw data from 'netCDF'...
rawEIC-methodsGet extracted ion chromatograms for specified m/z range
rawMat-methodsGet a raw data matrix
rectUniqueDetermine a subset of rectangles with unique, non-overlapping...
retcor-methodsCorrect retention time from different samples
retcor.obiwarp-methodsAlign retention times across samples with Obiwarp
retcor.peakgroups-methodsAlign retention times across samples
retexpSet retention time window to a specified width
sampnames-methodsGet sample names
specDist.cosine-methodsa Distance function based on matching peaks
specDist.meanMZmatch-methodsa Distance function based on matching peaks
specDist-methodsDistance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist.peakCount-methodsa Distance function based on matching peaks
specNoiseCalculate noise for a sparse continuum mass spectrum
specPeaksIdentify peaks in a sparse continuum mode spectrum
split.xcmsRawDivide an xcmsRaw object
split.xcmsSetDivide an xcmsSet object
SSgaussGaussian Model
stitch-methodsCorrect gaps in data
write.cdf-methodsSave an xcmsRaw object to file
write.mzdata-methodsSave an xcmsRaw object to a file
xcmsEIC-classClass xcmsEIC, a class for multi-sample extracted ion...
xcmsFileSource-classBase class for loading raw data from a file
xcmsFragmentsConstructor for xcmsFragments objects which holds Tandem MS...
xcmsFragments-classClass xcmsFragments, a class for handling Tandem MS and...
xcmsPeaks-classA matrix of peaks
xcmsRawConstructor for xcmsRaw objects which reads NetCDF/mzXML...
xcmsRaw-classClass xcmsRaw, a class for handling raw data
xcmsSetConstructor for xcmsSet objects which finds peaks in...
xcmsSet-classClass xcmsSet, a class for preprocessing peak data
xcmsSource-classVirtual class for raw data sources
xcmsSource-methodsCreate an 'xcmsSource' object in a flexible way
sneumann/xcms-presvnbridge documentation built on May 26, 2017, 1:25 p.m.