make.cytoscape.network: Drug and Pathway connection output files for Cytoscape...

In DrInsight: Drug Repurposing: Integration and Systematic Investigation of Genomic High Throughput Data

Description

This fucniton allows user to get the two files needed for Cytoscape to visulize the drug-pathway network

Usage

make.cytoscape.network(
  path.analysis.res = path.analysis.res,
  pathway.FDR.cutoff = 0.1
)

Arguments

path.analysis.res	The pathway analysis results. Output of pathway.analysis().
pathway.FDR.cutoff	The FDR threshold to select significant drug specific pathways and the default is 0.1.

Examples

## get the Dr. Insight drug identification results
drug.ident.res = drug.ident(query.data = example.disease, cmap.ref.profiles = example.drug.profiles,
                 repurposing.unit = "treatment", connectivity = "negative")

## load in example pathway data
data("example.pathway")

## Performe pathway analysis (for the drugs that are identified by ident.drug())
path.analysis.res = pathway.analysis(drug.ident.res = drug.ident.res,
                    pathway.list = example.pathway, drug.FDR.cutoff = 0.5)

## get the pathway analysis ouput that can be loaded into Cytoscape for visulization
network.cytoscape = make.cytoscape.network(path.analysis.res = path.analysis.res,
pathway.FDR.cutoff = 0.5)

DrInsight documentation built on July 8, 2020, 7:36 p.m.