calEdgeCorScore: Calculate the differential correlation score for edges

In ESEA: ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

Description

CalEdgeCorScore attempts to calculate the differential correlation scores of two genes in the edge between the expression data of all samples and control samples.

Usage

  calEdgeCorScore(dataset, class.labels, controlcharactor, edgesbackgrand)

Arguments

dataset	A marix of gene expression data whose row names are genes symbols and whose column names are samples.
class.labels	A vector of binary labels. The vector is used to distinguish the class of phenotype.
controlcharactor	A character string of control sample label.
edgesbackgrand	A marix which deposits the data of background set of edges.

Details

For each edge, we estimated the mutual information (MI) between two genes in the expression data of all samples and control samples respectively. The difference of MI between all samples and control samples is used as the differential correlation score of the edge.

Value

A vector. Each element is the differential correlation score of an edge and whose name correspond to edge ID in the background set of edges.

Author(s)

Junwei Han <[e-mail]>, Xinrui Shi<[e-mail]> and Chunquan Li <[e-mail]>

References

Margolin, A.A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Dalla Favera, R. and Califano, A. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC bioinformatics, 7 Suppl 1, S7.

Mani, K.M., Lefebvre, C., Wang, K., Lim, W.K., Basso, K., Dalla-Favera, R. and Califano, A. (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Molecular systems biology, 4, 169.

Examples

## Not run: 

#get example data
dataset<-GetExampleData("dataset")
class.labels<-GetExampleData("class.labels")
controlcharactor<-GetExampleData("controlcharactor")

#get the data for background set of edges
edgesbackgrand<-GetEdgesBackgrandData()

#Calculate the differential correlation score for edges
EdgeCorScore<-calEdgeCorScore(dataset, class.labels, controlcharactor, edgesbackgrand)

#print the top ten results to screen
EdgeCorScore[1:10]

#Each element is the differential correlation score of an edge and whose name correspond to
# the edge in the background set of edges.


## End(Not run)

Example output

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: XML
Loading required package: parmigene
    AANAT|ACLY    AANAT|ACSL1    AANAT|ACSL3    AANAT|ACSL4    AANAT|ACSL6 
   -0.05406403    -0.28411395    -0.07583330    -0.07442451     0.14375235 
    AANAT|ASMT      AANAT|DDC     AANAT|MAOA     AANAT|MAOB AANAT|SLC25A16 
   -0.24033758    -0.06331058    -0.10133133    -0.01922738     0.20428877 

ESEA documentation built on May 2, 2019, 3:41 p.m.