MicPathmatch

A function is used to trace the affiliation between microbes (16S or Metagenome data) and functional pathways based on Kyoto Encyclopedia of Gene and Genomes (KEGG).
You can get two tables using this function.
One is a table including predicted detail next level strains and pathways of your own microbes, the other is a table including only your own microbes and corresponding pathways.
The format of microbe is like this:
k__XXX; p__XXX; c__XXX; o__XXX; f__XXX; g__XXX; s__XXX;
k means kingdom;
p means phylum;
c means class;
o means order;
f means family;
g means genus;
s means species.

A strategy that provides the identification of metabolome and microbiome (Bi-omics) feature.
It is able to screen out key/driving features (metabolites, microbes, and pathway functions) by an integrated
importance score (IIS),combining sub-scores derived from difference, correlation, abundance, and network analysis.
It is able to identify microbe-function-metabolite chains and to rank association pairs within specific functions.

Tianlu Chen

BiOFI

Feature Identification Between Metabolome and Microbiome in
Disease and Health

MicPathmatch function

<dl><dt>microbes</dt>
<dd>A character vector containing the names of microbes.</dd></dl>

Arguments

MicPathmatch — MicPathmatch

<dl>

<dt>microbes</dt>
<dd>A character vector containing the names of microbes.</dd>

</dl>

MicPathmatch: MicPathmatch

Description

Usage

Value

Arguments

Examples