interactions {famat} | R Documentation

## Interactions between genes and metabolites

### Description

Gather informations about direct interactions between genes and metabolites inside a pathway, and about pathways themselves. These informations are direct interactions between these two elements and number of relations between an element from the list provided by the user and other elements of the pathway (centrality). Direct interactions extraction was performed using BioPax, KGML and GPML files parsed with PaxtoolsR, graphite and author's parsers.

### Usage

        interactions(listk, listr, listw)

### Arguments

`listk` | Output from `path_enrich` function, with "KEGG" argument.
`listr` | Output from `path_enrich` function, with "REAC" argument.
`listw` | Output from `path_enrich` function, with "WP" argument.

### Value

A list containing :

`size` | Dataframe containing pathways, genes and metabolites in pathways (from the list or not), and number of elements in pathways
`pathtot` | Dataframe containing pathways names and ids from pathway enrichment analysis on Reactome, Kegg and Wikipathways pathways
`tagged` | Dataframe containing direct interactions between elements from the user's list per pathways
`keggchebiname` | Dataframe containing all human metabolites ids (kegg and chebi) and names
`central` | List of pathways, each pathway containing the number of direct interactions between an element of user's list and other elements in the pathway
`no_path` | Dataframe containing direct interactions between elements from the user's list, but not per pathways
`genes` | User's genes given in `path_enrich` function
`meta` | User's metabolites given in `path_enrich` function

This list is used by `compl_data` function.

### Author(s)

Emilie Secherre emisecherre@gmail.com

### References

Luna, A., Babur, O., Aksoy, A. B, Demir, E., Sander, C. (2015).“PaxtoolsR: Pathway Analysis in R Using Pathway Commons.” Bioinformatics.

Sales G, Calura E, Cavalieri D, Romualdi C (2012). “graphite - a Bioconductor package to convert pathway topology to gene network.” BMC Bioinformatics. https://bmcbioinformatics.biomedcentral.com/articles/10 . 1186/1471-2105-13-20.

### See Also

`path_enrich` `compl_data`

### Examples

        ## load example data
        data(listk)
        data(listr)
        data(listw)

        interactions_result=interactions(listk,listr,listw)

[Package famat version 1.0.0 Index]