tni.sre {RTN} | R Documentation |
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.
tni.sre(object, sampleGroups, regulatoryElements = NULL, pValueCutoff = 0.05, pAdjustMethod = "BH")
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). |
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")
# 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)