AUEC: Calculate the area under the cumulative enrichment curve...

In TPEA: A Novel Topology-Based Pathway Enrichment Analysis Approach

Description

The interested gene set may be the differentially expressed genes or any other gene set. The function calculate the AUEC based on the interested genes. AUEC is the area under the cumulative enrichment curve in a coordinate system. X-axis displays the nodes by the scores from maximum to minimum. Y-axis displays the cumulative enrichment curve.

Usage

AUEC(DEGs)

Arguments

DEGs	The interested genes you input and the format must be "Entrez ID". If not,translate the interested genes into Entrez ID.

Details

The function only identifies Entrez ID of genes. The nodes are sorted by their AUEC in the pathway. If genes locates on the upstream or the nodes with high degree in a certain pathway, the AUEC of this pathway is high.

Value

The AUEC of 109 pathways based on the interested gene set.

Author(s)

Wei Jiang

Examples

##Randomly generated interested genes
DEGs<-sample(100:100000,15)
DEG<-as.matrix(DEGs);
## The function is used to calculate the observed statistic
area<-AUEC(DEG);

Example output

Loading required package: MESS
Loading required package: Matrix
Loading required package: foreach

TPEA documentation built on May 1, 2019, 8:13 p.m.