tni.sre: Subgroup Regulon Enrichment for TNI-class objects.

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

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)

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