Question: leading edge analysis clusterProfiler DOSE custom GSEA
1
gravatar for Riba Michela
3.1 years ago by
Riba Michela80
Riba Michela80 wrote:

Hi,

 

I’m writing about your very useful and complete packages for functional analysis.

In particular I often use DOSE and clusterProfiler and ChipSeeker.

 

I’m writing about the possibility to perform leading edge analysis in GSEA.

I found on your github page you have already developed this 

for gseDO() function in DOSE.

 

I’m interested in performing GSEA analysis using custom database and would like to perform also leading edge analysis.

 

I tried GSEA() in clusterProfiler but this does not perform leading edge analysis (in the stable bioconductor version)

 

and GSEA_internal() in DOSE, here I had additional problem because I cannot give a TERM2GENE table, instead

the option in the function is USER_DATA, which I was not able to reproduce and I did not found an explanation on how

should this field be provided.

Anyhow

 

could you suggest me the more practical way to be able to perform

 

custom GSEA analyis with leading edge analysis, perhaps without need to install the Development version of Bioconductor?

 

 

I thank you very much and look forward to your answer.

 

Michela Riba

 

 

 

 

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8

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

other attached packages:
[1] clusterProfiler_3.0.5 DOSE_2.10.7           pander_0.6.0         
[4] DT_0.2                plyr_1.8.4            VennDiagram_1.6.17   
[7] futile.logger_1.4.3   gplots_3.0.1          limma_3.28.21        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7          bitops_1.0-6         futile.options_1.0.0
 [4] tools_3.3.1          digest_0.6.10        lattice_0.20-34     
 [7] tibble_1.2           annotate_1.50.0      RSQLite_1.0.0       
[10] gtable_0.2.0         graph_1.50.0         igraph_1.0.1        
[13] DBI_0.5-1            parallel_3.3.1       SparseM_1.72        
[16] topGO_2.24.0         stringr_1.1.0        knitr_1.14          
[19] htmlwidgets_0.7      S4Vectors_0.10.3     gtools_3.5.0        
[22] caTools_1.17.1       IRanges_2.6.1        stats4_3.3.1        
[25] GSEABase_1.34.1      qvalue_2.4.2         Biobase_2.32.0      
[28] AnnotationDbi_1.34.4 XML_3.98-1.4         GOSemSim_1.30.3     
[31] gdata_2.17.0         tidyr_0.6.0          reshape2_1.4.1      
[34] GO.db_3.3.0          DO.db_2.9            ggplot2_2.1.0       
[37] lambda.r_1.1.9       magrittr_1.5         matrixStats_0.50.2  
[40] splines_3.3.1        scales_0.4.0         htmltools_0.3.5     
[43] BiocGenerics_0.18.0  assertthat_0.1       xtable_1.8-2        
[46] colorspace_1.2-6     KernSmooth_2.23-15   stringi_1.1.1       
[49] munsell_0.4.3    

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Riba Michela80
Answer: leading edge analysis clusterProfiler DOSE custom GSEA
0
gravatar for Guangchuang Yu
3.1 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:
On Mon, Oct 3, 2016 at 6:35 PM, Riba Michela [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Riba Michela <https: support.bioconductor.org="" u="" 6472=""/> wrote Question: > leading edge analysis clusterProfiler DOSE custom GSEA > <https: support.bioconductor.org="" p="" 87757=""/>: > > Hi, > > > > I’m writing about your very useful and complete packages for functional > analysis. > > In particular I often use DOSE and clusterProfiler and ChipSeeker. > > > > I’m writing about the possibility to perform leading edge analysis in GSEA. > > I found on your github page you have already developed this > > for gseDO() function in DOSE. > > > > I’m interested in performing GSEA analysis using custom database and would > like to perform also leading edge analysis. > > > > I tried GSEA() in clusterProfiler but this does not perform leading edge > analysis (in the stable bioconductor version) > > > You need to use the devel branch, see https://guangchuangyu.github.io/ggtree/faq/#could-not-find-function. > and GSEA_internal() in DOSE, here I had additional problem because I > cannot give a TERM2GENE table, instead > First of all, don't use internal function. For custom annotation, you need to use GSEA function in clusterProfiler. You need to prepare TERM2GENE table if you don't have one. You can't expect clusterProfiler to perform enrichment analysis without annotation, right? This is why TERM2GENE is *needed*. > the option in the function is USER_DATA, which I was not able to reproduce > and I did not found an explanation on how > > should this field be provided. > > Anyhow > > > > could you suggest me the more practical way to be able to perform > > > > custom GSEA analyis with leading edge analysis, perhaps without need to > install the Development version of Bioconductor? > > > > > > I thank you very much and look forward to your answer. > > > > Michela Riba > > ------------------------------ > > Post tags: clusterprofiler, DOSE, GSEA_internal, USER_DATA, leading edge > Analysis > > You may reply via email or visit leading edge analysis clusterProfiler DOSE custom GSEA > -- --~--~---------~--~----~------------~-------~--~----~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: https://guangchuangyu.github.io -~----------~----~----~----~------~----~------~--~---
ADD COMMENTlink written 3.1 years ago by Guangchuang Yu1.1k
Answer: leading edge analysis clusterProfiler DOSE custom GSEA
0
gravatar for Riba Michela
3.1 years ago by
Riba Michela80
Riba Michela80 wrote:

Oh sure, I have tried and as I told everything ok,

consider the question is

 

how could I perform leading edge analysis using clusterprofiler?

I tried the internal function just because I found the example gseDO in DOSE package, here:

http://guangchuangyu.github.io/2016/05/news-of-my-bioc-packages/

where the leading edge is mentioned as possible

 

could you please complete you kind answer?

 

thanks you so much

 

ADD COMMENTlink written 3.1 years ago by Riba Michela80

Do you really read my blog post?

Can you copy the sentence that mentioned leading edge analysis and paste it here?

 

 

 

 

ADD REPLYlink written 3.1 years ago by Guangchuang Yu1.1k
1

I *think* the OP has this link in mind: here. With the current release version of R/BioC, generating a cnetplot of the leading edge genes does indeed not work when using the example dataset/code provided on that page; likely because the output of gseDO() has been modified in development *only* to accommodate this functionality.

ADD REPLYlink written 3.1 years ago by Guido Hooiveld2.5k
Answer: leading edge analysis clusterProfiler DOSE custom GSEA
0
gravatar for Riba Michela
3.1 years ago by
Riba Michela80
Riba Michela80 wrote:

Hi, I found this stating from the page you mention

Leading edge analysis and core enriched genes

Leading edge analysis reports Tags to indicate the percentage of genes contributing to the enrichment score, List to indicate where in the list the enrichment score is attained and Signal for enrichment signal strength.

It would also be very interesting to get the core enriched genes that contribute to the enrichment.

r Biocpkg("DOSE") supports leading edge analysis and report core enriched genes in GSEA analysis.

 

below the exact place

https://github.com/GuangchuangYu/DOSE/blob/91db8c9d42859d3ac4b661fa0061d9563302f021/vignettes/GSEA.Rmd

and then used GSEA_internal of DOSE to do the same using custom database

then I found that probably this was in development bioconductor

could you please answer my question now?

How could I perform GSEA and leading edge analysis with custom database?

Which version of DOSE or cluster Profiler should I use

which Bioconductor version should I install

 

thanksa lot

 

meanwhile I consider the cnet option you mention, but I do not use frequently yhis functionality for enrichment

looking forward to your answer

 

Michela

 

 

 

 

ADD COMMENTlink written 3.1 years ago by Riba Michela80

already answered, see my previous post:

You need to use the devel branch, see https://guangchuangyu.github.io/ggtree/faq/#could-not-find-function.

 

 

First of all, don't use internal function. For custom annotation, you need to use GSEA function in clusterProfiler. You need to prepare TERM2GENE table if you don't have one. You can't expect clusterProfiler to perform enrichment analysis without annotation, right? This is why TERM2GENE is *needed*.

 

ADD REPLYlink written 3.1 years ago by Guangchuang Yu1.1k
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