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Hi,
How can I sort the clusterProfiler package results (groupGOResult object) for instance according GeneRatio in groupGO?
Thanks.
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Guangchuang Yu
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@guangchuang-yu-5419
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China/Guangzhou/Southern Medical Univer…
If for visualization, just pass order=TRUE to barplot. It will sort result based on count which is similar to geneRatio (since geneRatio = count/geneNum, and geneNum is identical).
You can use summary(groupGO_object) to export the result as a data.frame and sort it yourself if you want to do other things.
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sghoshucla
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@sghoshucla-13462
Last seen 6.8 years ago
How do I subset groupGO objects?
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Thanks Guangchuang Yu,
But this only sort displayed category (showCategory) not all category. I want plot 10 category with max count.
I use showCategory to subset the result first.
Will change to order result first, follow by subsetting. Then your question can be resolved by barplot(x, showCategory=10, order=T)
In current implementation, you can use the following script:
> df = summary(x)
> term=df$ID[order(df$Count, decreasing=T)]
> barplot(x, showCategory=term[1:10], order=T)