Package 'xcms' - Bioconductor

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12 fillPeaks.MSW-methods Value A xcmsSet objects with filled in peak groups (into and maxo). Methods object = "xcmsSet" fillPeaks.chrom(object, nSlaves=0) See Also xcmsSet-class, getPeaks fillPeaks fillPeaks.MSW-methods Integrate areas of missing peaks in FTICR-MS data Description For each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak. Arguments object the xcmsSet object Details After peak grouping, there will always be peak groups that do not include peaks from every sample. This method produces intensity values for those missing samples by integrating raw data in peak group region. In a given group, the start and ending m/z values for integration are defined by the median start and end points of the other detected peaks. Value A xcmsSet objects with filled in peak groups. Methods object = "xcmsSet" fillPeaks.MSW(object) See Also xcmsSet-class, getPeaks fillPeaks
findMZ 13 findMZ Find fragment ions in xcmsFragment objects Description This is a method to find a fragment mass with a ppm window in a xcmsFragment object Usage findMZ(object, find, ppmE=25, print=TRUE) Arguments object find ppmE print xcmsFragment object type The fragment ion to be found the ppm error window for searching If we should print a nice little report Details The method simply searches for a given fragment ion in an xcmsFragment object type given a certain ppm error window Value A data frame with the following columns: PrecursorMz The precursor m/z of the fragment MSnParentPeakID An index ID of the location of the precursor peak in the xcmsFragment object msLevel rt mz intensity sample The level of the found fragment ion the Retention time of the found ion the actual m/z of the found fragment ion The intensity of the fragment ion Which sample the fragment ion came from GroupPeakMSn an ID if the peaks were grouped by an xcmsSet grouping CollisionEnergy The collision energy of the precursor scan Author(s) H. Paul Benton,
Page 1 and 2: Package ‘xcms’ May 22, 2014 Ver
Page 3 and 4: absent-methods 3 specDist.cosine .
Page 5 and 6: c-methods 5 ob
Page 7 and 8: diffreport-methods 7 Details Value
Page 9 and 10: etg 9 tstat pvalue anova mzmed mzmi
Page 11: fillPeaks.chrom-methods 11 Details
Page 15 and 16: findneutral 15 Value A data frame w
Page 17 and 18: findPeaks.centWave-methods 17 findP
Page 19 and 20: findPeaks.massifquant-methods 19 Re
Page 21 and 22: findPeaks.matchedFilter-methods 21
Page 23 and 24: findPeaks.MS1-methods 23 findPeaks.
Page 25 and 26: getEIC-methods 25 Methods object =
Page 27 and 28: getScan-methods 27 getScan-methods
Page 29 and 30: group.density 29 group.density Grou
Page 31 and 32: group.nearest 31 group.nearest Grou
Page 33 and 34: groupval-methods 33 See Also xcmsSe
Page 35 and 36: medianFilter 35 Value A list contai
Page 37 and 38: peakPlots-methods 37 Examples msnfi
Page 39 and 40: plot.xcmsEIC 39 Examples ## Not run
Page 41 and 42: plotEIC-methods 41 plotEIC-methods
Page 43 and 44: plotrt-methods 43 Methods object =
Page 45 and 46: plotSurf-methods 45 plotSurf-method
Page 47 and 48: profRange-methods 47 profRange-meth
Page 49 and 50: awEIC-methods 49 rawEIC-methods Get
Page 51 and 52: etcor.obiwarp 51 Details Value Diff
Page 53 and 54: etexp 53 family plottype col ty if
Page 55 and 56: specDist.cosine 55 Value mzabs mzpp
Page 57 and 58: specDist.peakCount-methods 57 specD
Page 59 and 60: split.xcmsRaw 59 Value A matrix wit
Page 61 and 62: stitch-methods 61 Arguments x mu si
Page 63 and 64:
verify.mzQuantM 63 verify.mzQuantM
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write.mzQuantML-methods 65 write.mz
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xcmsFragments 67 Slots Extends .Dat
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xcmsPapply 69 Methods collect signa
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xcmsPeaks-class 71 results
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xcmsRaw 73 References NetCDF file f
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xcmsRaw-class 75 Methods Note findP
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xcmsSet-class 77 Details Value The
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xcmsSource-class 79 progressCallbac
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Index ∗Topic classes xcmsEIC-clas
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INDEX 83 fillPeaks, 3, 12, 77, 78 f
Page 85 and 86:
INDEX 85 plotScan (plotScan-methods
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INDEX 87 xcmsFileSource, 79 xcmsFil
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Package 'xcms' - Bioconductor

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