8 months ago by

United States

Here you go if you want to use fisher's exact test.

```
enrich.test = function(PathGenes, interestGenes, totalGenes) {
################################################
### | inPath | not inPath |
###-------------------------------------------
### Predict | a | b | nPredict
###notPredict | c | d |
###-------------------------------------------
### | nPath | | nAll
################################################
##remove genes not included in reference gene set
PathGenes = intersect(PathGenes,totalGenes)
interestGenes = intersect(interestGenes, totalGenes)
nPath <- length(PathGenes)
nPredict <- length(interestGenes)
a <- length(intersect(PathGenes,interestGenes))
b <- nPredict - a
c <- nPath - a
nAll = length(totalGenes)
d <- nAll - (a + b + c)
m <- matrix(c(a,b,c,d), ncol=2,byrow=T)
colnames(m) <- c('inPath','notInPath');rownames(m) <- c('Predict','notPredict')
p <- fisher.test(m,alternative='greater')$p.value
##using phyper for hypergeometric test
p1 <- phyper(a-1,nPath, nAll-nPath,nPredict,lower.tail=F)
p2 <-1 - phyper(a-1,nPath, nAll-nPath,nPredict)
tmp <- c(a,b,c,d,p,p1,p2)
res = list(mat=m,p=list('fisher.exact'=p,
'phyper1'=p1,
'phyper2'=p2),
overlapped=intersect(PathGenes, interestGenes))
res
}
```

•

link
modified 8 months ago
•
written
8 months ago by
ewre • **220**
The following tools will be helpful to achieve that.

https://bioconductor.org/packages/release/bioc/html/GSEABase.html

https://bioconductor.org/packages/release/bioc/html/fgsea.html

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