RTN (version 1.10.0)

tna.overlap: Overlap analysis over a list of regulons.

Description

This function takes a TNA object and returns the results of the overlap analysis among regulons in a transcriptional network (with multiple hypothesis testing corrections).

Usage

tna.overlap(object, pValueCutoff=0.05, pAdjustMethod="BH", minRegulonSize=15, tnet="ref",  tfs=NULL, verbose=TRUE)

Arguments

object

a preprocessed object of class 'TNA' TNA-class.

pValueCutoff

a single numeric value specifying the cutoff for p-values considered significant.

pAdjustMethod

a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details).

minRegulonSize

a single integer or numeric value specifying the minimum number of elements in a regulon that must map to elements of the gene universe. Gene sets with fewer than this number are removed from the analysis.

tnet

a single character value specifying which transcriptional network should to used to compute the overlap analysis. Options: "dpi" and "ref".

tfs

an optional vector with transcription factor identifiers.

verbose

a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

a data frame in the slot "results", see 'overlap' option in tna.get.

See Also

TNA-class

Examples

data(dt4rtn)

tfs4test<-c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")
rtni <- new("TNI", gexp=dt4rtn$gexp, transcriptionFactors=dt4rtn$tfs[tfs4test])

## Not run: 
# 
# rtni <- tni.preprocess(rtni,gexpIDs=dt4rtn$gexpIDs)
# rtni<-tni.permutation(rtni)
# rtni<-tni.bootstrap(rtni)
# rtni<-tni.dpi.filter(rtni)
# rtna<-tni2tna.preprocess(rtni, phenotype=dt4rtn$pheno, hits=dt4rtn$hits, phenoIDs=dt4rtn$phenoIDs)
# 
# #run overlap analysis pipeline
# rtna <- tna.overlap(rtna)
# 
# #get results
# tna.get(rtna,what="overlap")
# ## End(Not run)