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 MS data is available in
MetaboLights with accession number MTBLS8735. Details and settings for
the preprocessing are provided in the
Metabonaut
resource (end-to-end metabolomics data analysis workflow)
Louail et al.; Zenodo.
The data set contains two abundance matrices (assays):
"raw": the original quantified feature abunances representing the integrated peak areas of the identified chromatographic peaks."raw_filled": gap-filled feature abundance matrix. Same content as assay"raw"but with missing values replaced by the MS signal measured in the expected peak area for the respective ions/features.
Examples
## Load the data
data(se)
library(SummarizedExperiment)
## Access row (feature) data
rowData(se)
#> DataFrame with 9068 rows and 11 columns
#> mzmed mzmin mzmax rtmed rtmin rtmax npeaks
#> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
#> FT0001 50.9898 50.9893 50.9904 203.600 201.459 208.108 8
#> FT0002 51.0590 51.0581 51.0599 191.167 190.053 194.525 9
#> FT0003 51.9866 51.9863 51.9879 203.147 201.459 207.046 7
#> FT0004 53.0204 53.0161 53.0205 203.234 200.962 217.922 10
#> FT0005 53.5208 53.5184 53.5216 203.194 201.183 209.900 10
#> ... ... ... ... ... ... ... ...
#> FT9064 998.697 998.691 998.705 25.352 23.6341 26.4839 4
#> FT9065 998.779 998.758 998.784 162.691 161.5110 164.8667 8
#> FT9066 999.204 999.191 999.218 146.163 143.0103 147.9139 8
#> FT9067 999.330 999.318 999.339 157.048 154.3261 159.1735 7
#> FT9068 999.781 999.775 999.794 162.763 161.5110 164.3995 7
#> CTR CVD QC ms_level
#> <numeric> <numeric> <numeric> <integer>
#> FT0001 1 3 4 1
#> FT0002 2 3 4 1
#> FT0003 0 3 4 1
#> FT0004 3 3 4 1
#> FT0005 3 3 4 1
#> ... ... ... ... ...
#> FT9064 0 0 4 1
#> FT9065 2 2 4 1
#> FT9066 3 1 4 1
#> FT9067 3 1 3 1
#> FT9068 1 3 3 1
## List the available assays
assayNames(se)
#> [1] "raw" "raw_filled"