The se variable is a SummarizedExperiment::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