Kernel-Based Metabolomic Differential Analysis
This package implements a kernel-based score test in metabolomic differential analysis. In order to capture the special natural of metabolomic data, two new kernel functions are designed in this package. One is a distance-based kernel and the other is a stratified kernel. This kernel approach also allows set-level analysis. It can be use to test whether a set of metabolites (or a metabolite pathway) are differentially expressed under two conditions.
| Package: | KMDA |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2015-03-26 |
| License: | GPL(>=2) |
| Functions: | dkernel calcluates the distance-based kernel. |
| skernel calcluates the stratified kernel. | |
| dscore performs the distance-based kernel score test. | |
| sscore performs the stratified kernel score test. | |
| pearson.group performs the grouping of metabolites into metabolite-set based on Pearson correlation. | |
| spearman.group performs the grouping of metabolites into metabolite-set based on Spearman correlation. | |
Xiang Zhan and Debashis Ghosh
Maintainer: Xiang Zhan <xiangzhan9@gmail.com>
Zhan, X., Patterson, A. D., & Ghosh, D. (2015). Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data. BMC Bioinformatics, 16(1), 77.
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