Description Usage Format Details Source References See Also Examples
xcmsSet
object from the data in the paper on "Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites."
It was collected in positive ionization mode.
1 |
The format is:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | Formal class 'xcmsSet' [package "xcms"] with 12 slots
..@ peaks : num [1:83861, 1:23] 361 369 447 277 372 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:23] "mz" "mzmin" "mzmax" "rt" ...
..@ groups : logi[0 , 0 ]
..@ groupidx : list()
..@ filled : int(0)
..@ phenoData :'data.frame': 16 obs. of 2 variables:
.. ..$ Factor.Value.genotype. : Factor w/ 2 levels "Col-0","cyp79": 1 1 1 1 2 2 2 2 1 1 ...
.. ..$ Factor.Value.replicate.: Factor w/ 2 levels "Exp1","Exp2": 1 1 1 1 1 1 1 1 2 2 ...
..@ rt :List of 2
.. ..$ raw :List of 16
.. .. ..$ : num [1:3562] 0.562 0.898 1.235 1.572 1.908 ...
.. .. ..$ : num [1:3570] 0.57 0.907 1.244 1.58 1.917 ...
.. .. ..$ : num [1:3564] 0.823 1.159 1.496 1.833 2.236 ...
.. .. ..$ : num [1:3566] 0.501 0.838 1.175 1.511 1.848 ...
.. .. ..$ : num [1:3565] 0.514 0.851 1.187 1.524 1.861 ...
.. .. ..$ : num [1:3566] 0.73 1.07 1.4 1.74 2.08 ...
.. .. ..$ : num [1:3567] 0.513 0.85 1.187 1.523 1.86 ...
.. .. ..$ : num [1:3568] 0.499 0.836 1.173 1.509 1.846 ...
.. .. ..$ : num [1:3567] 0.53 0.866 1.203 1.54 1.876 ...
.. .. ..$ : num [1:3567] 0.672 1.008 1.345 1.682 2.019 ...
.. .. ..$ : num [1:3568] 0.604 0.94 1.277 1.614 1.95 ...
.. .. ..$ : num [1:3566] 0.514 0.85 1.187 1.524 1.86 ...
.. .. ..$ : num [1:3568] 0.511 0.848 1.184 1.521 1.858 ...
.. .. ..$ : num [1:3567] 0.483 0.82 1.156 1.493 1.83 ...
.. .. ..$ : num [1:3567] 0.508 0.844 1.181 1.518 1.855 ...
.. .. ..$ : num [1:3568] 0.48 0.817 1.154 1.491 1.827 ...
.. ..$ corrected:List of 16
.. .. ..$ : num [1:3562] 0.562 0.898 1.235 1.572 1.908 ...
.. .. ..$ : num [1:3570] 0.57 0.907 1.244 1.58 1.917 ...
.. .. ..$ : num [1:3564] 0.823 1.159 1.496 1.833 2.236 ...
.. .. ..$ : num [1:3566] 0.501 0.838 1.175 1.511 1.848 ...
.. .. ..$ : num [1:3565] 0.514 0.851 1.187 1.524 1.861 ...
.. .. ..$ : num [1:3566] 0.73 1.07 1.4 1.74 2.08 ...
.. .. ..$ : num [1:3567] 0.513 0.85 1.187 1.523 1.86 ...
.. .. ..$ : num [1:3568] 0.499 0.836 1.173 1.509 1.846 ...
.. .. ..$ : num [1:3567] 0.53 0.866 1.203 1.54 1.876 ...
.. .. ..$ : num [1:3567] 0.672 1.008 1.345 1.682 2.019 ...
.. .. ..$ : num [1:3568] 0.604 0.94 1.277 1.614 1.95 ...
.. .. ..$ : num [1:3566] 0.514 0.85 1.187 1.524 1.86 ...
.. .. ..$ : num [1:3568] 0.511 0.848 1.184 1.521 1.858 ...
.. .. ..$ : num [1:3567] 0.483 0.82 1.156 1.493 1.83 ...
.. .. ..$ : num [1:3567] 0.508 0.844 1.181 1.518 1.855 ...
.. .. ..$ : num [1:3568] 0.48 0.817 1.154 1.491 1.827 ...
..@ filepaths : chr [1:16] "/usr/local/lib/R/site-library/mtbls2//vol/R/BioC/devel/mtbls2/MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818.mzData" "/usr/local/lib/R/site-library/mtbls2//vol/R/BioC/devel/mtbls2/MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820.mzData" "/usr/local/lib/R/site-library/mtbls2//vol/R/BioC/devel/mtbls2/MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822.mzData" "/usr/local/lib/R/site-library/mtbls2//vol/R/BioC/devel/mtbls2/MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824.mzData" ...
..@ profinfo :List of 2
.. ..$ method: chr "bin"
.. ..$ step : num 0.1
..@ dataCorrection : int(0)
..@ polarity : chr(0)
..@ progressInfo :List of 12
.. ..$ group.density : num 0
.. ..$ group.mzClust : num 0
.. ..$ group.nearest : num 0
.. ..$ findPeaks.centWave : num 0
.. ..$ findPeaks.massifquant : num 0
.. ..$ findPeaks.matchedFilter: num 0
.. ..$ findPeaks.MS1 : num 0
.. ..$ findPeaks.MSW : num 0
.. ..$ retcor.obiwarp : num 0
.. ..$ retcor.peakgroups : num 0
.. ..$ fillPeaks.chrom : num 0
.. ..$ fillPeaks.MSW : num 0
..@ progressCallback:function (progress)
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The corresponding raw mzData files are located in the mzData
subdirectory of this package.
http://www.ebi.ac.uk/metabolights/MTBLS2 https://github.com/sneumann/mtbls2
Neumann, S., Thum, A. & Böttcher, C. Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data Metabolomics (2012) DOI: 10.1007/s11306-012-0401-0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | data(mtbls2)
## The directory with the mzData LC/MS files
filepath <- file.path(find.package("mtbls2"), "mzData")
filepath
list.files(filepath, recursive = TRUE)
if (require(xcms)) {
## xcmsSet Summary
show(mtbls2Set)
filepaths(mtbls2Set)[1]
## Access raw data file
## Not run:
xr <- xcmsRaw(filepaths(mtbls2Set)[1], profmethod = "bin", profstep = 0.1)
xr
## End(Not run)
}
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