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Last data update: 2014.03.03

R: Produce augmented pathways

integrate_mir

R Documentation

Produce augmented pathways

Description

This function takes each pathway of the input list of signaling pathways and adds the miRNAs that are related to it.

Usage

integrate_mir(original_pathways, targets_db)

Arguments

original_pathways

A list of graph::graphNEL objects where each of the nodes is named with '<gene_ID>'. Gene IDs used to identify the nodes must be the same gene IDs used to identify the genes on the miRNA-target interactions data.frame, targets_db. i.e. If the genes are identified by Entrez ID on the original_pathways graph::graphNEL list, then the targets_db data.frame must identify the genes by Entrez ID as well. Nodes of each graph::graphNEL represent the genes involved in the pathway and edges represent the biological interactions (activation or repression) among those genes (activation or repression).

targets_db

A data.frame with columns: 'miRNA' which names the miRNAs and 'Target.ID' which gives the gene ID of the target gene. The Gene IDs used to identify the "Target.ID" column must be the same gene IDs used on the nodes of the original_pathways. i.e. If the genes are identified by Entrez ID on the original_pathways graph::graphNEL list, then the targets_db data.frame must identify the genes by Entrez ID as well.

Value

Gene signaling pathways augmented with miRNA interactions. This is a list of graph::graphNEL objects where each of the nodes is named with '<gene_ID>'. Nodes of each graph::graphNEL represent genes and miRNAs involved in the pathway and edges represent the biological interactions (activation or repression) among them.

Author(s)

Diana Diaz <dmd at wayne dot edu>

Examples

data(kegg_pathways)
data(mirTarBase)
kegg_pathways <- kegg_pathways[1:5] #delete this for augmenting all pathways.
augmented_pathways <- integrate_mir(kegg_pathways, mirTarBase)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mirIntegrator)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirIntegrator/integrate_mir.Rd_%03d_medium.png", width=480, height=480)
> ### Name: integrate_mir
> ### Title: Produce augmented pathways
> ### Aliases: integrate_mir
> 
> ### ** Examples
> 
> data(kegg_pathways)
> data(mirTarBase)
> kegg_pathways <- kegg_pathways[1:5] #delete this for augmenting all pathways.
> augmented_pathways <- integrate_mir(kegg_pathways, mirTarBase)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>