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    

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

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