Optimaldrugs {DRviaSPCN}

Identifying the optimal drugs

Description

Function "Optimaldrugs" used to identify the optimal drugs for specific disease.

Usage

Optimaldrugs(ExpData,Label,DrugSPESC,CentralityScore,nperm=1000,
                   topcut=10,pcut=0.01,weight=FALSE)

Arguments

ExpData

A gene expression profile of interest (rows are genes, columns are samples).

Label

A character vector consist of "0" and "1" which represent sample class in gene expression profile. "0" means normal sample and "1" means disease sample.

DrugSPESC

A matrix with n rows and m columns. n is the number of subpathways and m is the number of all drugs. The values in this matrix is weighted enrichmentscore of subpathways induced by each drug. The users could obtain this matrix from our example data.

CentralityScore

The result of function "CalCentralityScore".

nperm

Number of random permutations (default: 1000).

topcut

The parameter "topcut" represents the number of selected SPs from the top or bottom of the ranked SP list. The topcut defaults to 10.

pcut

The parameter "pcut" represents the threshold of statistical significance for screen SPs. The pcut defaults to 0.01.

weight

A boolean value determines the method for calculating the drug-disease association score of the drug. "weight=FALSE"(default): Similar to "CMap" (Lamb et al., 2006), no weight is needed. "weight=TRUE": KS random walk statistic with individualized subpathway activity score as weight was used to calculate the drug-disease reverse association score.

Value

A dataframe with four columns which are "Drug"(drug names),"DES"(drug enrichment score),"p-value"(statistical significance),"FDR"(adjusted statistical significance).

Examples

##Obtain input data
#Weighted enrichmentscore of subpathways induced by each drug were stored
#in package "DRviaSPCNData". "DRviaSPCNData" has been uploaded to the
#github repository.Users can download and install through "install_github"
#function and set parameter url="hanjunwei-lab/DRviaSPCNData".
#After installing and loading package "DRviaSPCNData",
#users can use the following command to get the data.
#DrugSPESCMatrix<-GetData('DrugSPESCMatrix')
CentralityScoreResult<-GetExample("CentralityScoreResult")
GEP<-GetExample("GEP")
Slabel<-GetExample("Slabel")
#Run the function
#Opdrugresult<-Optimaldrugs(ExpData=GEP,Label=Slabel,DrugSPESC=DrugSPESCMatrix,
#CentralityScore=CentralityScoreResult,nperm=1000,topcut=10,pcut=0.01,weight=FALSE)