help with clusterProfiler enricher function
2
1
Entering edit mode
@naholialejandri-9269
Last seen 4.1 years ago
Mexico

Hello, I started an enrichment analysis but I'am stuck with the enrichment part, my organism is not in the list of supported organisms so I made my custom annotation. When I use the enricher function I just get a NA vector, what am I doing wrong?

 

> require(clusterProfiler)
> gene=as.vector(read.table('test.txt'))
> gene <- as.vector(gene[,1])
> head(gene)
[1] "TR8693|c0_g1"  "TR21614|c0_g1" "TR9528|c0_g1"  "TR27994|c0_g1"
[5] "TR21705|c1_g1" "TR20654|c0_g2"
> 
> gda <- read.delim("GO_full.txt")
> dim(gda)
[1] 61552     4
> head(gda)
     geneID       goID                  description           ontology
1 TR1|c0_g1 GO:0005737                    cytoplasm cellular_component
2 TR1|c0_g1 GO:0005829                      cytosol cellular_component
3 TR1|c0_g1 GO:0005654                  nucleoplasm cellular_component
4 TR1|c0_g1 GO:0005634                      nucleus cellular_component
5 TR1|c0_g1 GO:0022624 proteasome accessory complex cellular_component
6 TR1|c0_g1 GO:0000502           proteasome complex cellular_component
> 
> term2gene=gda[, c("goID", "geneID")]
> term2desc=gda[, c("goID", "description")]
> 
> 
> x = enricher(gene, TERM2GENE=term2gene, TERM2NAME=term2desc)
> head(summary(x))
     Mode      NA's 
"logical"       "1" 

 

Please help me. Thanks in advace.

 

 
clusterprofiler • 1.3k views
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5
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 4 months ago
China/Guangzhou/Southern Medical Univer…

 No enriched result is a valid result.

 

You can set pvalueCutoff=1, qvalueCutoff=1, minGSSize =1 to get the full result without cutting pvalue and qvalue.

 

 

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@naholialejandri-9269
Last seen 4.1 years ago
Mexico

Thank you so much, I thought I was committing a syntax error. But it was rather in the interpretation of the result. It was very helpful.

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