perform.ijPairs.FET: Fisher Exact Test (FET) analysis for user specific pairs of...

In songw01/MEGENA: Multiscale Clustering of Geometrical Network

Fisher Exact Test (FET) analysis for user specific pairs of gene sets

Description

FET with given pairs

Usage

  perform.ijPairs.FET(geneSets1,geneSets2,ij,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.
ij	two column integer matrix. Each row contains a pair of indices to compare between geneSet1 and geneSet2. For instance, ij[1,] = c(1,2), then FET is performed between geneSets1[[1]] and geneSets2[[2]].
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.AllPairs.FET, this function is designed to perform FET on a specified set of comparisons to save time.

Author(s)

Won-Min Song

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