Question: hyperGTest with org.Sc.sgd.db problem
0
gravatar for andrejk
3.9 years ago by
andrejk0
andrejk0 wrote:

I try to annotate ENTREZID identifiers with GO categories and apply hyperGTest() function. Using the following example from https://support.bioconductor.org/p/64862/ everything works fine:

library(org.Sc.sgd.db)
univ <- unique(keys(org.Sc.sgd.db))
genes <- univ[sample(1:length(univ), 250)]
p <- new("GOHyperGParams", geneIds = genes, universeGeneIds = univ, ontology = "BP", annotation = "org.Sc.sgd.db")
hyp <- hyperGTest(p)
head(summary(hyp))

I have no idea what are keys in the presented example. How can I instead use ENTREZID identifiers as keys in my testing?

go bioconductor R • 900 views
ADD COMMENTlink modified 3.9 years ago by EagleEye6.6k • written 3.9 years ago by andrejk0
0
gravatar for EagleEye
3.9 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

Try this tool,

Gene Set Clustering based on Functional annotation (GeneSCF)

ADD COMMENTlink written 3.9 years ago by EagleEye6.6k
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