spikedApples: Metabolomics data on spiked apples

In BioMark: Find Biomarkers in Two-Class Discrimination Problems

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")

Example output

Loading required package: pls

Attaching package: ‘pls’

The following object is masked from ‘package:stats’:

    loadings

Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.0-2
Loading required package: MASS
Loading required package: st
Loading required package: sda
Loading required package: entropy
Loading required package: corpcor
Loading required package: fdrtool

BioMark documentation built on May 2, 2019, 3:01 a.m.