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        

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.

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

Thank you very much for your help.

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

Marcus