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Does enrichGO support “ENSEMBL” format? #588
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Please use the latest version of clusterProfiler and get the document by |
It has been a while that you posted this question, but since your genes are in ENSEMBL-format: why then not use the available GO annotations from ENSEMBL in combination with the generic function Below some example code for tomato that I adapted from one of my 'plant projects'. Also: some code snippets from this book chapter gave me a kick-start for the
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example code continued.
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Hello,
I am a beginner of bioinformatics and am using enrichGO to analyze up-regulated genes in tomato. My genes are in ensemble format (e.g. Solyc01g005730.3), but when I run
It says: Error in get_GO_data(OrgDb, ont, keyType) : keytype is not supported...
But, based on this website: https://guangchuangyu.github.io/2016/01/go-analysis-using-clusterprofiler/, my gene format should work. Can anyone please help?
I also tried to convert it to different format using the following code whichcauses great loss of information.
Some ID occurs one-to-many match, like "Solyc01g059965.1"
44.67% genes are mapped to entrezid
100% genes are mapped to ensembl
2.33% genes are mapped to symbol
Any thoughts or suggestions would be greatly appreciated!
Thank you!
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