perform.AllPairs.FET: Fisher Exact Test (FET) analysis for ALL possible pairs of...

In songw01/MEGENA: Multiscale Clustering of Geometrical Network

Fisher Exact Test (FET) analysis for ALL possible pairs of two gene set lists.

Description

FET for all pairs.

Usage

  perform.AllPairs.FET(geneSets1,geneSets2,background,adjust.FET.pvalue = T)

Arguments

geneSets1	a list object containing gene signatures as character vector in each list entry.
geneSets2	a list object containing gene signatures as character vector in each list entry.
background	a character vector containing the background gene set.
adjust.FET.pvalue	If set TRUE, bonferroni correction is performed and output in corrected.FET.pvalue column.

Details

Returns a data.frame entailing all comparisons.

Value

In comparison to perform.ijPairs.FET, this function is designed to perform FET on ALL comparisons.

Author(s)

Won-Min Song

Examples

## Not run: 
rm(list = ls())
data(Sample_Expression)
data(FrequentSets.v6.2)
ijw <- calculate.correlation(datExpr[1:100,],doPerm = 2)
el <- calculate.PFN(ijw[,1:3])
g <- graph.data.frame(el,directed = FALSE)
MEGENA.output <- do.MEGENA(g = g,remove.unsig = FALSE,doPar = FALSE,n.perm = 10)
output.summary <- MEGENA.ModuleSummary(MEGENA.output,
mod.pvalue = 0.05,hub.pvalue = 0.05,
min.size = 10,max.size = 5000,
annot.table = NULL,id.col = NULL,symbol.col = NULL,
output.sig = TRUE)

FET.results = perform.AllPairs.FET(geneSets1 = output.summary$modules,geneSets2 = msigdb.sets[[2]],background = V(g)$name)
FET.results = FET.results[order(FET.results$FET_pvalue),]
head(FET.results)


## End(Not run)

songw01/MEGENA documentation built on Jan. 19, 2024, 6:51 p.m.