Package 'xcms' - Bioconductor

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26 getPeaks-methods Methods object = "xcmsRaw" getEIC(object, mzrange, rtrange = NULL, step = 0.1) object = "xcmsSet" getEIC(object, mzrange, rtrange = 200, groupidx, sampleidx = sampnames(obje See Also xcmsRaw-class, xcmsSet-class, xcmsEIC-class getPeaks-methods Get peak intensities for specified regions Description Integrate extracted ion chromatograms in pre-defined defined regions. Return output similar to findPeaks. Arguments object peakrange step the xcmsSet object matrix or data frame with 4 columns: mzmin, mzmax, rtmin, rtmax (they must be in that order or named) step size to use for profile generation Value A matrix with columns: i mz mzmin mzmax ret retmin retmax into intf maxo maxf rank of peak identified in merged EIC (
getScan-methods 27 getScan-methods Get m/z and intensity values for a single mass scan Description Return the data from a single mass scan using the numeric index of the scan as a reference. Arguments object scan mzrange the xcmsRaw object integer index of scan. if negative, the index numbered from the end limit data points returned to those between in the range, range(mzrange) Value A matrix with two columns: mz intensity m/z values intensity values Methods object = "xcmsRaw" getScan(object, scan, mzrange = numeric()) getMsnScan(object, scan, mzrange = numeri See Also xcmsRaw-class, getSpec getSpec-methods Get average m/z and intensity values for multiple mass scans Description Return full-resolution averaged data from multiple mass scans. Arguments Details object the xcmsRaw object ... arguments passed to profRange used to sepecify the spectral segments of interest for averaging Based on the mass points from the spectra selected, a master unique list of masses is generated. Every spectra is interpolated at those masses and then averaged.
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 and 12: fillPeaks.chrom-methods 11 Details
Page 13 and 14: findMZ 13 findMZ Find fragment ions
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: getEIC-methods 25 Methods object =
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
Page 65 and 66: write.mzQuantML-methods 65 write.mz
Page 67 and 68: xcmsFragments 67 Slots Extends .Dat
Page 69 and 70: xcmsPapply 69 Methods collect signa
Page 71 and 72: xcmsPeaks-class 71 results
Page 73 and 74: xcmsRaw 73 References NetCDF file f
Page 75 and 76: xcmsRaw-class 75 Methods Note findP
Page 77 and 78:
xcmsSet-class 77 Details Value The
Page 79 and 80:
xcmsSource-class 79 progressCallbac
Page 81 and 82:
Index ∗Topic classes xcmsEIC-clas
Page 83 and 84:
INDEX 83 fillPeaks, 3, 12, 77, 78 f
Page 85 and 86:
INDEX 85 plotScan (plotScan-methods
Page 87:
INDEX 87 xcmsFileSource, 79 xcmsFil
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