fisherTest,character,list,character-method | R Documentation |
Perform Fisher's exact test on a GeneSet object
## S4 method for signature 'character,list,character'
fisherTest(
genes,
genesets,
universe,
makeUniqueNonNA = TRUE,
checkUniverse = TRUE,
useEASE = FALSE
)
genes |
a collection of genes of which over-representation of the gene set is tested |
genesets |
A |
universe |
universe of genes |
makeUniqueNonNA |
Logical, whether genes and universe should be filtered to remove NA and made unique. The default is set to |
checkUniverse |
Logical, if |
useEASE |
Logical, whether to use the EASE method to report the p-value. This function performs one-sided Fisher's exact test to test the over-representation of gene set genes in the input gene list. |
myGenes <- LETTERS[1:3]
myS4GeneSet1 <- list(name="GeneSet1", desc="GeneSet",
genes=LETTERS[1:6], namespace="My namespace 1")
myS4GeneSet2 <- list(name="GeneSet1", desc="GeneSet",
genes=LETTERS[2:7], namespace="My namespace 2")
myUniverse <- LETTERS
fisherTest(myGenes, myS4GeneSet1, myUniverse)
fisherTest(myGenes, myS4GeneSet2, myUniverse)
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