Performing GO analysis from Differential Peaks
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Entering edit mode
12 months ago

Hello everyone, I called for FindMarkers() in order to find differential peaks between two biological conditions and the following was output ("diff.peaks").

My question is how would I generate a nice chart for GO analysis from this? My current code is:

install.packages("JASPAR2022")
library(JASPAR2022)
library(JASPAR2020)
library(clusterProfiler)

    go_enrichment <- enrichGO(diff.peaks, universe = rownames(exc_subset),
                          OrgDb = "org.Mm.eg.db", keyType = "GENEID",
                          ont = "BP", pvalueCutoff = 0.05, qvalueCutoff = 0.05)

enter image description here

The following image is what I have. No q-value, so how would I change the parameters of "go_enrichment" to successfully carry this out?

clusterProfiler Signac analysis atac-seq go • 294 views
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