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  • Enrichment GO analysis with R on an ordered list

    Hello all!

    I'm trying to perform a gene set enrichment analysis from RNA-seq data on an ordered gene list, that is, a gene list with logFC or p-values. I want the analysis to get into account not only the genes with the highest or lowest values but also all values in the middle of this list (tools that manage this are FATISCAN or DAVID I think).

    My problem is to find something similar as an R-package. Because of technical problems it is not suitable for me to work with R-packages that link to graphical interfaces.

    Do you know about tools like that?

    Greets )

  • #2
    Your question is not very clear.

    As far as I know, you can use DAVID to do a gene ontology enrichment analysis, not a gene set enrichment analysis. If I am wrong, someone please correct me.
    I use DAVID to do gene ontology enrichment analyses, and therefore provide only the genes with the "highest or lowest values".
    There is an R package to interface with DAVID called RDAVIDWebService.

    If you want to do a gene set enrichment analysis on the entire ranked gene list, without using a graphical user interface, you can just call the JAR file for GSEA from the command line. If you're really fond of R, you can call the command to use the GSEA JAR file from R, and process the output directly in R, with a custom script.

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