interactions: Interactions between genes and metabolites

In emiliesecherre/famat: Functional analysis of metabolic and transcriptomic data

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 [e-mail]

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)

emiliesecherre/famat documentation built on April 23, 2023, 9:15 p.m.