tni.overlap.genesets {RTN} | R Documentation

## Associate regulons with external gene set collections.

### 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)

[Package RTN version 2.16.0 Index]