Affiliation:
1. MRC Integrative Epidemiology Unit at the University of Bristol , Bristol BS8 1TH, UK
2. Population Health Science, Bristol Medical School, University of Bristol , Bristol BS8 1TH, UK
3. NIHR Bristol Biomedical Research Centre, University of Bristol , Bristol BS8 1TH, UK
4. Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust , Bradford BD9 6RJ, UK
Abstract
Abstract
Motivation
Metabolomics is an increasingly common part of health research and there is need for preanalytical data processing. Researchers typically need to characterize the data and to exclude errors within the context of the intended analysis. Whilst some preprocessing steps are common, there is currently a lack of standardization and reporting transparency for these procedures.
Results
Here, we introduce metaboprep, a standardized data processing workflow to extract and characterize high quality metabolomics datasets. The package extracts data from preformed worksheets, provides summary statistics and enables the user to select samples and metabolites for their analysis based on a set of quality metrics. A report summarizing quality metrics and the influence of available batch variables on the data are generated for the purpose of open disclosure. Where possible, we provide users flexibility in defining their own selection thresholds.
Availability and implementation
metaboprep is an open-source R package available at https://github.com/MRCIEU/metaboprep.
Supplementary information
Supplementary data are available at Bioinformatics online.
Funder
Medical Research Council Integrative Epidemiology Unit
University of Bristol
UK Medical Research Council
British Heart Foundation Doctoral Training Program
National Institute for Health Research
Biomedical Centre at the University Hospitals Bristol NHS Foundation Trust
Wellcome Trust
Avon Longitudinal Study of Parents and Children
University of Bristol NIHR Biomedical Research Centre
MRC Integrative Epidemiology Unit
CRUK Integrative Cancer Epidemiology Programme
UK British Heart Foundation
National Institute of Health
European Research Council
British Heart Foundation Chair
National Institute of Health Research Senior Investigator
UK Economic and Social Science Research Council
British Heart Foundation
Publisher
Oxford University Press (OUP)
Subject
Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability