path_enrich {famat} | R Documentation

## Pathway enrichment analysis

### Description

Perform a pathway enrichment analysis using a list of genes and a list of metabolites. Pathways enrichment analysis is performed using MPINet for metabolites and gprofiler2 for genes.

### Usage

        path_enrich(source, metabo, genes)

### Arguments

`source` | Pathways database used, either Kegg ("KEGG"), Reactome ("REAC") or Wikipathays ("WP")
`metabo` | Dataframe with three columns : the first column contain the list of metabolites, the second some quantitative data about the metabolites, the last one words "DOWN" or "UP" depending on the metabolites concentration behavior in a certain condition. Last two columns can contain only/some NAs. All metabolites ids are KEGG Compound ids.
`genes` | Dataframe with three columns : the first column contain the list of genes, the second some quantitative data about the genes, the last one words "DOWN" or "UP" depending on the genes expression behavior in a certain condition. Last two columns can contain only/some NAs. All genes ids are gene symbol.

### Value

A list containing :

`resmeta` | Results of metabolites pathway enrichment analysis
`resgene` | Results of genes pathway enrichment analysis
`genes` | Vector containing genes
`metabo` | Vector containing metabolites

This list is used by `interactions` function.

### Author(s)

Emilie Secherre emisecherre@gmail.com

### References

Yanjun Xu, Chunquan Li and Xia Li (2013). MPINet: The package can implement the network-based metabolite pathway identification of pathways.. R package version 1.0. https://CRAN.R-project.org/package=MPINet

Liis Kolberg and Uku Raudvere (2020). gprofiler2: Interface to the 'g:Profiler' Toolset. R package version 0.2.0. https://CRAN.R-project.org/package=gprofiler2

### See Also

`interactions`

### Examples

        ## load example data
        data(genes)
        data(meta)

        ## perform pathway enrichment analysis on Reactome pathways
        listr=path_enrich("REAC", meta, genes)

[Package famat version 1.0.0 Index]