Package 'xcms' - Bioconductor

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34 loadRaw-methods image-methods Plot log intensity image of a xcmsRaw object Description Create log intensity false-color image of a xcmsRaw object plotted with m/z and retention time axes Arguments x xcmsRaw object col vector of colors to use for for the image ... arguments for profRange Methods x = "xcmsRaw" image(x, col = rainbow(256), ...) Author(s) Colin A. Smith, See Also xcmsRaw-class loadRaw-methods Read binary data from a source Description This function extracts the raw data which will be used an xcmsRaw object. Further processing of data is done in the xcmsRaw constructor. Arguments object Specification of a data source (such as a file name or database query) Details The implementing methods decide how to gather the data.
medianFilter 35 Value A list containing elements describing the data source. The rt, scanindex, tic, and acquisitionNum components each have one entry per scan. They are "parallel" in the sense that rt[1], scanindex[1], and acquisitionNum[1] all refer to the same scan. The list containst he following components: rt tic scanindex mz intensity Numeric vector with acquisition time (in seconds) for each scan Numeric vector with Total Ion Count for each scan Integer vector with starting positions of each scan in the mz and intensity components. It is an exclusive offset, so scanindex[i] is the offset in mz and intensity before the beginning of scan i. This means that the mz (respectively intensity) values for scan i would be from scanindex[i] + 1 to scanindex[i + 1] Concatenated vector of m/z values for all scans Concatenated vector of intensity values for all scans Methods signature(object = "xcmsSource") Uses loadRaw,xcmsSource-method to extract raw data. Subclasses of xcmsSource can provide different ways of fetching data. Author(s) Daniel Hackney, See Also xcmsRaw-class, xcmsSource medianFilter Apply a median filter to a matrix Description For each element in a matix, replace it with the median of the values around it. Usage medianFilter(x, mrad, nrad) Arguments x mrad nrad numeric matrix to median filter number of rows on either side of the value to use for median calculation number of rows on either side of the value to use for median calculation
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 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: groupval-methods 33 See Also xcmsSe
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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