Description Usage Arguments Value Author(s) Examples
Performs advanced gene set enrichment analysis on a set of genes.
1 2 | setRankAnalysis(geneIDs, setCollection, use.ranks = TRUE, setPCutoff = 0.01,
fdrCutoff = 0.05, delete = TRUE)
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geneIDs |
A vector containing the set of gene IDs to test for gene set enrichment. This is typically the list of significant genes returned by the analysis of an omics dataset. |
setCollection |
A gene set collection object, generated with the
|
use.ranks |
Logical value indicating if the |
setPCutoff |
The p-value cutoff to be used to consider a gene set significant. Recommended value: 0.01 |
fdrCutoff |
The cutoff to be applied on the corrected p-value after false-positive sets have been removed. |
delete |
A flag indicating if non-significant gene sets should be deleted, which is the behaviour that you want. It is best to ignore this argument, it was only added for debugging purposes. |
An igraph object. Use the igraph get.data.frame
function to get a data frame with all the significant gene sets.
Cedric Simillion
1 2 3 4 5 6 7 8 9 10 11 | options(mc.cores=1)
reference = sprintf("gene_%03d", 1:50)
geneSets = lapply(1:9, function(i) sample(reference[((i-1)*5):((i+1)*5)], 5))
annotationTable = data.frame(termID=sprintf("set_%02d", rep(1:9, each=5)),
geneID=unlist(geneSets),
termName = sprintf("dummy gene setet %d", rep(1:9, each=5)),
dbName = "dummyDB",
description = "A dummy gene set DB for testing purposes")
collection = buildSetCollection(annotationTable, referenceSet=reference)
genes = reference[sample(c(TRUE, FALSE), 50, TRUE)]
network = setRankAnalysis(genes, collection, TRUE)
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