edges {G1DBN}R Documentation

Edges listing and evaluation

Description

This function allows to order the edges by decreasing likelihood. ROC curves can also be computed if a validation matrix is specified.

Usage

out<-edges(score,predNames=NULL,targetNames=NULL,validMat=NULL,roc=FALSE,
threshold=1, nb=NULL, prec=3)

Arguments

score matrix with r columns (=target genes) and d rows (=predictor genes) containing the scores resulting from an estimation procedure (either inferG1 or GfromG1).
predNames An optional array (d) giving a list of names for the predictor genes, default=NULL.
targetNames An optional array (r) giving a list of names for the target genes, default=NULL.
validMat An optional matrix specifying the validated edges (1 if an edge is validated, 0 otherwise).
roc Boolean, TRUE wether ROC curves should be computed, default=NULL. This option require to specify a validation matrix validMat.
threshold An optional real setting the maximal value for edge selection, default=1.
nb An optional integer setting the maximal number of selected edges, default=NULL.
prec An optional integer setting the number of decimal places for score display, default=3.

Value

A list with out$ref and out$names matrices containing a list of edges ordered by decreasing likelihood (First column: parent, second column: child, third column: the corresponding score). If a validation matrix validMat is specified, a 4th column indicates wether the edge is validated (1 for a validated edge, 0 otherwise).
out$ref lists edges according to the index value of each variable and out$names uses the names from arrays predNames and targetNames.
out$rocx and out$rocy contain the coordinates for plotting ROC curves if a validation matrix is specified.

Author(s)

Lebre Sophie (http://stat.genopole.cnrs.fr/~slebre).

See Also

inferG1, GfromG1.

Examples

#generate AR(1) time series 
AR<-simulAR1(p=10,n=50,edgeProp=0.02,minA=0.5,maxA=1.5,minB=0,maxB=1,minSig=0.1,maxSig=0.8)
AR

# compute score S1
pmaxG1<-inferG1(AR$data, ls=TRUE, tukey=FALSE, huber=FALSE, predictor=NULL, target=NULL)
pmaxG1$ls
# compute score S2 from S1
Gls<-GfromG1(pmaxG1$ls, AR$data, method='ls',alpha1=0.2,alpha2=1,predictor=NULL,
target=NULL)
Gls$score

### Results (The validation matrix is obtained from the simulation matrix AR$A). 
resG1<-edges(score=pmaxG1$ls, targetNames=NULL, predNames=NULL,
validMat = (abs(AR$A)>0)*1, roc=TRUE, threshold=1, nb=NULL, prec=4)
resG<-edges(score=Gls$S2, targetNames=NULL, predNames=NULL,
validMat=(abs(AR$A)>0)*1, roc=TRUE, threshold=1, nb=NULL, prec=4)

# Edges list
resG1$list
resG$list

# ROC curve
plot(resG1$rocx/max(resG1$rocx),resG1$rocy/max(resG1$rocy), type="l",
 xlab="False Positive", ylab="True Positive", main="ROC curve")
lines(resG$rocx/max(resG$rocx), resG$rocy/max(resG$rocy), col=2,lty=2)
leg=c("Step 1", "Step 2")
legend(0.8,0.2, leg, lty=c(1,2), col=c(1,2))

[Package G1DBN version 1.0 Index]