mtbls213: xcmsSet for MTBLS213

In jcapelladesto/geoRge: Isotopic label tracking for untargeted metabolomics

Description

LC/MS data from a human retinal pigment epithelium cell line (ARPE-19) grown on normal and high glucose concentrations that mimics diabetic retinopathy conditions in vitro.

Usage

data("mtbls213")

Format

The format is: Formal class 'xcmsSet' [package "xcms"] with 14 slots ..@ peaks : num [1:205594, 1:11] 169 169 169 169 173 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:11] "mz" "mzmin" "mzmax" "rt" ... ..@ groups : num [1:14607, 1:11] 100 100 100 100 101 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:11] "mzmed" "mzmin" "mzmax" "rtmed" ... ..@ groupidx :List of 14607 .. ..$ : int [1:12] 4940 14904 26709 36721 67803 77949 88441 152196 159043 186197 ... [...] .. ..$ : int [1:12] 5704 16678 27596 37577 48785 58589 68787 79316 90029 101538 ... .. .. [list output truncated] ..@ filled : int [1:80267] 125328 125329 125330 125331 125332 125333 125334 125335 125336 125337 ... ..@ phenoData :'data.frame': 12 obs. of 1 variable: .. ..$ class: Factor w/ 4 levels "CELL_Glc12_05mM_Normo",..: 1 1 1 2 2 2 3 3 3 4 ... ..@ rt :List of 2 .. ..$ raw :List of 12 .. .. ..$ : num [1:5023] 2.23 2.48 2.73 2.98 3.23 ... [...] .. .. ..$ : num [1:5024] 2.15 2.4 2.65 2.9 3.15 ... .. ..$ corrected:List of 12 .. .. ..$ : num [1:5023] 2.21 2.46 2.72 2.97 3.22 ... [...] .. .. ..$ : num [1:5024] 2.21 2.46 2.72 2.97 3.22 ... ..@ filepaths : chr [1:12] "/home/sneumann/src/R/geoRgeProject/MTBLS213/CELL_Glc12_05mM_Normo_04.mzXML" "/home/sneumann/src/R/geoRgeProject/MTBLS213/CELL_Glc12_05mM_Normo_05.mzXML" "/home/sneumann/src/R/geoRgeProject/MTBLS213/CELL_Glc12_05mM_Normo_06.mzXML" "/home/sneumann/src/R/geoRgeProject/MTBLS213/CELL_Glc12_25mM_Normo_16.mzXML" ... ..@ 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 1 .. ..$ retcor.peakgroups : num 0 .. ..$ fillPeaks.chrom : num 0 .. ..$ fillPeaks.MSW : num 0 ..@ progressCallback:function (progress) ..@ mslevel : num(0) ..@ scanrange : num(0)

Details

Obtained by

setwd("../MTBLS213/")

xset <- xcmsSet(method="centWave", ppm=30, peakwidth=c(5,20)) sampclass(xset) <- substring(sampnames(xset), 1, 21)

xset2 <- retcor(xset,method="obiwarp", profStep=0.1) xset3 <- group(xset2, mzwid=0.0065, minfrac=0.5, bw= 4) xset3 <- fillPeaks(xset3)

Source

http://www.ebi.ac.uk/metabolights/MTBLS213

References

"geoRge: a computational tool for stable isotope labelling detection in LC/MS-based untargeted metabolomics"

Jordi Capellades, Miriam Navarro, Sara Samino, Marta Garcia-Ramirez, Cristina Hernandez, Rafael Simo, Maria Vinaixa and Oscar Yanes

Analytical Chemistry. 2016.

Examples

data(mtbls213)
mtbls213

jcapelladesto/geoRge documentation built on Sept. 18, 2021, 2:05 p.m.