path_enrich: Pathway enrichment analysis

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

View source: R/path_enrich.R

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

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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

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

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

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