| spikedApples {BioMark} | R Documentation |
Metabolomics data on spiked apples
Description
An data set of LC-MS features, obtained from twenty apples. The last ten apples are spiked with known compounds. This set provides a test case for biomarker selection methods: the task is to retrieve the true biomarker variables. The raw LC-MS data have been converted to CDF format and processed with XCMS to obtain the features.
Usage
data(spikedApples)Format
The format is a list of four elements:
- mz
the m/z values of the features (rounded)
- rt
the retention times of the features
- dataMatrix
the intensities of the features in the individual samples
- biom
the indices of the "true" biomarkers
Author(s)
Pietro Franceschi
References
P. Franceschi, D. Masuero, U. Vrhovsek, F. Mattivi and R. Wehrens: A benchmark spike-in data set for biomarker identification in metabolomics. J. Chemom. 26, 16-24 (2012)
R. Wehrens, P. Franceschi, U. Vrhovsek and F. Mattivi. Stability-based biomarker selection. Analytica Chimica Acta (2011), 705, 15-23. http://dx.doi.org/10.1016/j.aca.2011.01.039.
Examples
data(spikedApples)
## show features identified in all apples
plot(spikedApples$rt, spikedApples$mz,
xlab = "Retention time (s)", ylab = "m/z",
main = "Spiked apples - subset")