KMDA-package: Kernel-Based Metabolomic Differential Analysis

In KMDA: Kernel-Based Metabolite 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.

Author(s)

Xiang Zhan and Debashis Ghosh
Maintainer: Xiang Zhan <[e-mail]>

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.

KMDA documentation built on May 2, 2019, 3:59 p.m.