tni.sre {RTN} | R Documentation

## Subgroup Regulon Enrichment for TNI-class objects.

### Description

This method evaluates which regulons are enriched in sample groups, given a grouping variable. It performs Fisher's Exact Test whether a regulon is positively or negatively enriched in a subgroup using regulon activity.

### Usage

    tni.sre(object, sampleGroups, regulatoryElements = NULL,
            pValueCutoff = 0.05, pAdjustMethod = "BH")

### Arguments

`object` | A TNI object.
`sampleGroups` | either a list featuring sample groups or a string indicating a group varible available in the TNI object.
`regulatoryElements` | an optional string vector specifying regulons to use for the analysis.
`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).

### Value

A TNI-class object with the results of the subgroup regulon enrichment added to the results slot. To recover the results, use tni.get(object, "regulonEnrichment")

### See Also

`tni.plot.sre`

### Examples

    # load tniData
    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)

    #run GSEA2 analysis pipeline
    rtni <- tni.gsea2(rtni)

    # set sample groups
    colAnnotation <- tni.get(rtni, "colAnnotation")
    sampleGroups <- list(G1=colAnnotation$ID[1:60],
                    G2=colAnnotation$ID[61:90],
                    G3=colAnnotation$ID[91:120])

    # run subgroup regulon enrichment analysis
    rtni <- tni.sre(rtni, sampleGroups)

    # get results
    tni.get(rtni, "subgroupEnrichment")

    # for a heatmap representation, see the tni.plot.sre() function.

    ## End(Not run)

[Package RTN version 2.18.0 Index]