Problem with BuildGOmap() in clusterProfiler
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Marcus • 0
@marcus-11917
Last seen 4.3 years ago

Hi,

so I am quite new to R but used clusterProfiler allready for KEGG enrichment analysis.

Now I would like to use it for GO enrichment analysis. Since the organism I am working witch is not supported I need to build my own GO mapping  and tried to do that by usingthe buildGOmap() function. And there is my problem, which I am unable to fix, even after a couple of days of reading and trying.

Since I am working witch a diatom, I get my gene to GO mapping from EnsemblProtist. I downloaded it, modified it so there are only entrezgeneID in the list which have a GO accession number and saved it as a tab-deliminated text file. Than I load it into R and proceed with the code as follows:

library(clusterProfiler)

gomap<-read.delim("c:/........../gomapping.txt", colClasses="character") 
head(gomap)

go_accession entrezgene
1   GO:0016020    7194683
2   GO:0016021    7194683
3   GO:0003735    7194684
4   GO:0005622    7194684
5   GO:0005840    7194684
6   GO:0006412    7194684

 

buildGOmap(gomap)

 

No error is actually produced. After the buildGO is excecuted it takes a long time and it gives out a long list in the console.

              GO    Gene
1      GO:0016020 7194683
2      GO:0016021 7194683
3      GO:0005575 7194683

.............

But its does nothing else. It does not produce the EG2ALLGO.rda ect. files in the working directory.

I tried many different stuff than just showed above in the code, but didnt make it work.

I think my problem is in how I give the data into the buildGOmap() function, but I just don't see the error.

It would be very nice if someone could help me and send me in the right direction

Thanks

Marcus

 

 

I use RStudio

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] clusterProfiler_3.2.6 DOSE_3.0.9           

loaded via a namespace (and not attached):
 [1] igraph_1.0.1         Rcpp_0.12.8          AnnotationDbi_1.36.0 magrittr_1.5         splines_3.3.2       
 [6] BiocGenerics_0.20.0  IRanges_2.8.1        munsell_0.4.3        BiocParallel_1.8.1   colorspace_1.3-1    
[11] fastmatch_1.0-4      stringr_1.1.0        plyr_1.8.4           tools_3.3.2          parallel_3.3.2      
[16] grid_3.3.2           Biobase_2.34.0       data.table_1.9.6     gtable_0.2.0         DBI_0.5-1           
[21] assertthat_0.1       lazyeval_0.2.0       tibble_1.2           GOSemSim_2.0.2       gridExtra_2.2.1     
[26] tidyr_0.6.0          reshape2_1.4.2       DO.db_2.9            ggplot2_2.2.0        S4Vectors_0.12.0    
[31] qvalue_2.6.0         RSQLite_1.0.0        stringi_1.1.2        fgsea_1.0.2          GO.db_3.4.0         
[36] scales_0.4.1         stats4_3.3.2         chron_2.3-47        

 

 

 

 

 

clusterprofiler • 1.3k views
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1
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

The output of buildGOmap is the input (TERM2GENE) of enricher, see https://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/

 

No data will be saved.

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Marcus • 0
@marcus-11917
Last seen 4.3 years ago

Dear Guangchuang,

thank you for your reply. I understood your answer, tried it out and it indeed works nicely with the enricher function.

 

I did not mention in my first post but actually, I wanted to use the enrichGO function as a next step, like you described in your vignette "How to use clusterProfiler to do GO enrichment analysis with unsupported organisms" For me this way has two main advanteges. First I don't have to make the TERM2NAME annotation for the GO Terms seperately and second in the enrichGO function the ontology argument is implemented, which for me is a very important feature.

Could you again be so nice and send me in the right direction.

 

Thank you very much

Marcus

 

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the buildGOmap -> enrichGO workflow had been changed to buildGOmap( optional and only for GO) -> enricher.

Unfortunately, the previous workflow is not supported anymore.

The vignette you mentioned was pretty old, the last version that support this workflow was in BioC 2.13, https://bioconductor.org/packages/2.13/bioc/html/clusterProfiler.html and it was removed since BioC 2.14.

The go2ont and go2term helper functions may help you to separate GO sub-ontology and prepare TERM2NAME data.frame, see https://guangchuangyu.github.io/clusterProfiler/#useful-utilities

 

 

 

 

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Entering edit mode
Marcus • 0
@marcus-11917
Last seen 4.3 years ago

Thank you very much for your help.

With those two helper functions I'm quite confident I can make it work.

 

Marcus

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