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The se variable is a SummarizedExperiment() object representing the results from a xcms-based pre-processing of an LC-MS untargeted metabolomics data set. The raw data files are provided in the faahKO package. The pre-processing of this data set is described in detail in the xcms vignette of the xcms package. This object was created from the XCMSnExp result object with the quantify method.

Examples


## Load the data
data(se)

library(SummarizedExperiment)

## Access row (feature) data
rowData(se)
#> DataFrame with 225 rows and 11 columns
#>           mzmed     mzmin     mzmax     rtmed     rtmin     rtmax    npeaks
#>       <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
#> FT001     200.1     200.1     200.1   2901.63   2880.73   2922.53         2
#> FT002     205.0     205.0     205.0   2789.39   2782.30   2795.36         8
#> FT003     206.0     206.0     206.0   2788.73   2780.73   2792.86         7
#> FT004     207.1     207.1     207.1   2718.12   2713.21   2726.70         7
#> FT005     219.1     219.1     219.1   2518.82   2517.40   2520.81         3
#> ...         ...       ...       ...       ...       ...       ...       ...
#> FT221    591.30     591.3     591.3   3005.03   2992.87   3006.05         5
#> FT222    592.15     592.1     592.3   3022.11   2981.91   3107.59         6
#> FT223    594.20     594.2     594.2   3418.16   3359.10   3427.90         3
#> FT224    595.25     595.2     595.3   3010.15   2992.87   3013.77         6
#> FT225    596.20     596.2     596.2   2997.91   2992.87   3002.95         2
#>              KO        WT            peakidx  ms_level
#>       <numeric> <numeric>             <list> <integer>
#> FT001         2         0  287, 679,1577,...         1
#> FT002         4         4     47,272,542,...         1
#> FT003         3         4     32,259,663,...         1
#> FT004         4         3     19,249,525,...         1
#> FT005         1         2  639, 788,1376,...         1
#> ...         ...       ...                ...       ...
#> FT221         2         3    349,684,880,...         1
#> FT222         1         3     86,861,862,...         1
#> FT223         1         2  604, 985,1543,...         1
#> FT224         2         3     67,353,876,...         1
#> FT225         0         2  866,1447,1643,...         1