Package 'xcms' - Bioconductor

More documents

Recommendations

Info

46 profMethod-methods Value If ident == TRUE, an integer vector with the indecies of the points that were identified. Otherwise a two-column matrix with the plotted points. Methods object = "xcmsRaw" plotTIC(object, ident = FALSE, msident = FALSE) See Also xcmsRaw-class profMedFilt-methods Median filtering of the profile matrix Description Apply a median filter of given size to a profile matrix. Arguments object massrad scanrad the xcmsRaw object number of m/z grid points on either side to use for median calculation number of scan grid points on either side to use for median calculation Methods object = "xcmsRaw" profMedFilt(object, massrad = 0, scanrad = 0) See Also xcmsRaw-class, medianFilter profMethod-methods Get and set method for generating profile data Description These methods get and set the method for generating profile (matrix) data from raw mass spectral data. It can currently be bin, binlin, binlinbase, or intlin. Methods object = "xcmsRaw" profMethod(object) See Also xcmsRaw-class, profMethod, profBin, plotSpec, plotChrom, findPeaks
profRange-methods 47 profRange-methods Specify a subset of profile mode data Description Specify a subset of the profile mode matrix given a mass, time, or scan range. Allow flexible user entry for other functions. Arguments Details Value object mzrange rtrange scanrange the xcmsRaw object single numeric mass or vector of masses single numeric time (in seconds) or vector of times single integer scan index or vector of indecies ... arguments to other functions This function handles selection of mass/time subsets of the profile matrix for other functions. It allows the user to specify such subsets in a variety of flexible ways with minimal typing. Because R does partial argument matching, mzrange, scanrange, and rtrange can be specified in short form using m=, s=, and t=, respectively. If both a scanrange and rtrange are specified, then the rtrange specification takes precedence. When specifying ranges, you may either enter a single number or a numeric vector. If a single number is entered, then the closest single scan or mass value is selected. If a vector is entered, then the range is set to the range() of the values entered. That allows specification of ranges using shortened, slightly non-standard syntax. For example, one could specify 400 to 500 seconds using any of the following: t=c(400,500), t=c(500,400), or t=400:500. Use of the sequence operator (:) can save several keystrokes when specifying ranges. However, while the sequence operator works well for specifying integer ranges, fractional ranges do not always work as well. A list with the folloing items: mzrange masslab massidx scanrange scanlab scanidx rtrange timelab numeric vector with start and end mass textual label of mass range integer vector of mass indecies integer vector with stat ane end scans textual label of scan range integer vector of scan range numeric vector of start and end times textual label of time range
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 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: plotSurf-methods 45 plotSurf-method
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

Package 'xcms' - Bioconductor

Create successful ePaper yourself

Delete template?

Save as template?