lilikoi.meta_path

Performs single variate linear regression between selected pathways and each of their metabolites.
Output the network plot between pathways and metabolties.

A comprehensive analysis tool for metabolomics data. It consists a variety of functional modules, including several new modules: a pre-processing module for normalization and imputation, an exploratory data analysis module for dimension reduction and source of variation analysis, a classification module with the new deep-learning method and other machine-learning methods, a prognosis module with cox-PH and neural-network based Cox-nnet methods, and pathway analysis module to visualize the pathway and interpret metabolite-pathway relationships. References: H. Paul Benton <http://www.metabolomics-forum.com/index.php?topic=281.0> Jeff Xia <https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R> Travers Ching, Xun Zhu, Lana X. Garmire (2018) <doi:10.1371/journal.pcbi.1006076>.

Lana Garmire

lilikoi

Metabolomics Personalized Pathway Analysis Tool

Xinying Fang

Yu Liu

Zhijie Ren

Fadhl Alakwaa

Sijia Huang

lilikoi.meta_path function

<dl><dt>PDSmatrix</dt>
<dd>Pathway deregulation score matrix</dd>
<dt>selected_Pathways_Weka</dt>
<dd>Selected top pathways from the featureSelection function</dd>
<dt>Metabolite_pathway_table</dt>
<dd>Metabolites mapping table</dd>
<dt>pathway</dt>
<dd>interested pathway name</dd></dl>

Arguments

Metabolite-pathway regression — lilikoi.meta_path

<dl>

<dt>PDSmatrix</dt>
<dd>Pathway deregulation score matrix</dd>


<dt>selected_Pathways_Weka</dt>
<dd>Selected top pathways from the featureSelection function</dd>


<dt>Metabolite_pathway_table</dt>
<dd>Metabolites mapping table</dd>


<dt>pathway</dt>
<dd>interested pathway name</dd>

</dl>

lilikoi.meta_path: Metabolite-pathway regression

Description

Usage

Value

Arguments