Thank you very much!
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Hi all!
I have a list of 16 elements each containing DEx genes between our control and experimental groups
I would like to do enrichment analysis using enrichGO function from clusterProfiler for each (total 16). How can I apply enrichGO function on each of these from the list (using lapply or for loop in R) so I don't have to do it individually 16 times.
The goal is to get a new list with 16 elements each containing enrichGO results for each of the elements from DEG list.
Can someone help with the code?
Thank you!!
Using for loop:
GOres = list() # define an empty list to store the for loop output from each interation
for(i in 1:length(DEG)) {
GOres[[i]] = enrichGO(gene = DEG[[i]],
universe = allExpressedGene, #provide all genes with expression in your experiment/or skip this
OrgDb = org.Hs.eg.db, # assumed the data is coming from human
ont = "CC", # check other options like MF and BP
pAdjustMethod = "BH",
pvalueCutoff = 0.01,
qvalueCutoff = 0.05,
readable = TRUE)
}
Thank you very much!
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