Question

How to use clusterProfiler to do GO enrichment analysis with unsupported organisms

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Didi ▴ 10

@didi-10905

Last seen 2.7 years ago

Spain

Hi,

Following an old vignette on "How to use clusterProfiler to do GO enrichment analysis with unsupported organisms" I've got this error.

library(clusterProfiler)
> Gff2GeneTable("all.gff3", compress=T)
Reading all.gff3: found 813788 rows with classes: character, character, character, integer, integer, character, character, character, character
Error in merge.data.frame(GeneID, geneInfo, by.x = "GeneID", by.y = "GeneID") :
negative length vectors are not allowed

My aim is to use buildGOmap to prepare the annotation files for enrichGO function.

Thanks a lot.

D

clusterprofiler go Gff2GeneTable buildgo unsupported organisms • 2.4k views

ADD COMMENT • link 8.0 years ago Didi ▴ 10

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that vignette is pretty old and was remove since BioC 2.14.

Please see also <A: Problem with BuildGOmap() in clusterProfiler>

ADD REPLY • link 8.0 years ago Guangchuang Yu ★ 1.2k

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Thanks a lot. Is there any new function for parsing GFF file?

ADD REPLY • link 8.0 years ago Didi ▴ 10

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No. This function is previous design for translating gene ID for bacteria only and not well tested. I think I should remove it from future release.

ADD REPLY • link 8.0 years ago Guangchuang Yu ★ 1.2k

score 0 · Answer 1 · 2016-11-30

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Didi ▴ 10

@didi-10905

Last seen 2.7 years ago

Spain

Thanks again.

Sorry again. Is there any way to use the enrichGO function for unsupported organisms. I also want to use the ontology argument. You said that the go2ont and go2term helper functions may help the separate GO sub_ontology and prepare TERM2NAME data.frame but I couldn't figure out how.

ADD COMMENT • link 8.0 years ago Didi ▴ 10