KMDA (version 1.0)

KMDA-package: Kernel-Based Metabolomic Differential Analysis

Description

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.

Details

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.

References

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.