tni.bootstrap {RTN} | R Documentation |
This function takes a TNI object and returns the consensus transcriptional network.
tni.bootstrap(object, nBootstraps=100, consensus=95, parChunks=NULL, verbose=TRUE)
object |
a processed object of class 'TNI' |
nBootstraps |
a single integer or numeric value specifying the number of bootstraps for deriving a consensus between every TF-target association inferred in the mutual information analysis. If running in parallel, nBootstraps should be greater and multiple of parChunks. |
consensus |
a single integer or numeric value specifying the consensus fraction (in percentage) under which a TF-target association is accepted. |
parChunks |
an optional single integer value specifying the number of bootstrap chunks to be used in the parallel analysis. |
verbose |
a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE) |
a matrix in the slot "results" containing a reference transcriptional network,
see 'tn.ref' option in tni.get
.
Mauro Castro
data(tniData) ## Not run: # preprocessing rtni <- tni.constructor(expData=tniData$expData, regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), rowAnnotation=tniData$rowAnnotation) # linear version! rtni <- tni.permutation(rtni) rtni <- tni.bootstrap(rtni) ## parallel version with SNOW package! #library(snow) #options(cluster=snow::makeCluster(3, "SOCK")) #rtni <- tni.permutation(rtni) #rtni <- tni.bootstrap(rtni) #stopCluster(getOption("cluster")) ## End(Not run)