tni.overlap.genesets: Associate regulons with external gene set collections.

In RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Description

This function tests the overlap between gene sets and regulons.

Usage

tni.overlap.genesets(object, geneSetList, regulatoryElements = NULL, 
    minGeneSetSize = 15, sizeFilterMethod="posORneg",
    method = c("HT","JC"), pValueCutoff = 0.05, 
    pAdjustMethod = "BH", verbose = TRUE)

Arguments

object	a preprocessed object of class 'TNI' TNI-class already evaluated by the tni.dpi.filter method.
geneSetList	a list with gene sets.
regulatoryElements	a vector of valid regulatory elements (e.g. transcription factors).
minGeneSetSize	a single integer or numeric value specifying the minimum number of elements in a gene set that must map to elements of the gene universe. Gene sets with fewer than this number are removed from the analysis.
sizeFilterMethod	a single character value specifying the use of the 'minGeneSetSize' argument, which is applyed to regulon's positive and negative targets. Options: "posANDneg", "posORneg", "posPLUSneg". For "posANDneg", the number of both positive and negative targets should be > 'minGeneSetSize'; for "posORneg", the number of either positive or negative targets should be > 'minRegulonSize'; and for "posPLUSneg", the number of all targets should be > 'minGeneSetSize'.
method	a string specifying the method used to assess the association between gene sets and regulons (see 'Details').
pValueCutoff	a single numeric value specifying the cutoff for p-values considered significant (this parameter only affects the 'HT' option).
pAdjustMethod	a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details) (this parameter only affects the 'HT' option).
verbose	a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Details

The 'HT' option assesses the overlap between gene sets and regulons using a hypergeometric test, and returns a data frame with the overlap statistics. The 'JC' option assesses the overlap between gene sets and regulons using the Jaccard Coefficient (JC), and retuns a matrix with JC values.

Value

Either a data frame or a numeric matrix with association statistics between gene sets vs. regulons.

Author(s)

Mauro Castro

See Also

TNI-class

Examples

data(tniData)

## Not run: 

#compute regulons
rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)
rtni <- tni.permutation(rtni)
rtni <- tni.bootstrap(rtni)
rtni <- tni.dpi.filter(rtni)

#load a gene set collection 
#here, we build three random gene sets for demonstration
geneset1 <- sample(tniData$rowAnnotation$SYMBOL,50)
geneset2 <- sample(tniData$rowAnnotation$SYMBOL,50)
geneset3 <- sample(tniData$rowAnnotation$SYMBOL,50)
geneSetList <- list(geneset1=geneset1,
                    geneset2=geneset2,
                    geneset3=geneset3)

#run the overlap analysis
ovstats <- tni.overlap.genesets(rtni, geneSetList, pValueCutoff = 1)


## End(Not run)

RTN documentation built on Nov. 12, 2020, 2:02 a.m.