pseudoDrift

pseudoDrift is an R package to address technical errors, particularly signal drift and batch effects, commonly encountered in large-scale liquid chromatography-mass spectroscopy (LC-MS) metabolomic studies. The package offers the following key features:

1. Data simulation: pseudoDrift can simulate LC-MS metabolomic data, allowing researchers to test and validate their data processing and analysis methods.

2. Outlier detection: The package includes tools for identifying outliers in LC-MS metabolomic data, which can help researchers identify and remove problematic data points.

3. Training and testing approach: pseudoDrift introduces a new approach for capturing and optionally correcting technical errors in LC-MS metabolomic data. This procedure is designed to be flexible and adaptable to the researcher's specific needs.

The authors demonstrate the effectiveness of pseudoDrift by comparing its performance to existing methods using simulated data. They also showcase the package's utility by applying it to a targeted LC-MS dataset that profiles 33 phenolic compounds from seedling stem tissue in 602 genetically diverse non-transgenic maize inbred lines. This dataset offers a valuable resource for studying the dynamics of specialized metabolism in plants.