interactions: Interactions between genes and metabolites

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/interactions.R

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

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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

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emiliesecherre/famat documentation built on Dec. 1, 2020, 9:34 p.m.