getCNADEscore: getCNADEscore

In hanjunwei-lab/CNA2Subpathway: Identification of Dysregulated Subpathway Driven by Copy Number Alteration

Description

The function getCNADEscore used calculate the CNA-DEscore.we use Student’s t-test method to compute the gene differentially expressed level between CNA labels. To compare the genes regulated by CNAs at a common level, we convert the t-test p-value of each gene to z-score.

Usage

getCNADEscore(inexpData, CNALabel)

Arguments

inexpData	Gene Expression profile(GEP)
CNALabel	The CNA label (the result of function getCNAlabel)

Value

A matrix of the Student’s t-test result and CNA-DEscore

Examples

# obtain GEP data
GEP<-GetExampleData("GEP")
# obtain the result of getCNAlabel function
CNAlabelresult<-GetExampleData("CNAlabelresult")
# Calculate the CNA-DEscore
CNADEscore<-getCNADEscore(GEP,CNAlabelresult)
# view first the ten gene CNA-DEscore
head(CNADEscore[1:10,])

hanjunwei-lab/CNA2Subpathway documentation built on Jan. 28, 2021, 6:56 p.m.