CEG.network.graph: Plot The Pathway-CEG Network for A Drug

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

Description

This function allows user to plot the pathway-CEG network for a specified pathway in a specified drug.

Usage

CEG.network.graph(
  path.analysis.res = path.analysis.res,
  pathway.FDR.cutoff = 0.1,
  drug.name = NULL,
  pathway.name = NULL,
  show.plot = TRUE
)

Arguments

path.analysis.res	The pathway analysis results. Output of function pathway.analysis().
pathway.FDR.cutoff	The FDR threshold to select significant drug specific pathways and the default is 0.1.
drug.name	The name of the drug user would like to analyze.The specified drug name should among those that are listed in the output table of function network.graph().
pathway.name	The name of the pathway user would like to analyze. The specified pathway name should among those that are listed in the output table of function network.graph().
show.plot	True or False, specifying if you want to show the pathway-CEG plot for a specific drug and pathway.

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)

path.CEG.network = CEG.network.graph(path.analysis.res = path.analysis.res,
                  pathway.FDR.cutoff = 0.5,drug.name = "drug1",
                  pathway.name = "pathway5", show.plot = TRUE)

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