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How to install kegga for edgeR?

Anyone knows how to install the kegga package for edgeR?

The only thing that I can find from the web is this github address https://github.com/Bioconductor-mirror/limma/blob/master/man/goana.Rd, but "copy path" on this page actually does nothing.

Thanks in advance for your help!

rna-seq r software error gene
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updated by WouterDeCoster WouterDeCoster • written by dr.genetics dr.genetics

The former -- I don't have kegga installed yet. I know how to use it, though -- I think. :)

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written by dr.genetics dr.genetics

As @WouterDeCoster mentioned you can see in edgeR manual that kegga() is a function already embedded in edgeR.

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written by Farbod Farbod

1 answer

You don't have to install it, it comes together with edgeR. If you installed edgeR (and loaded the library) the function is also loaded.

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written by WouterDeCoster WouterDeCoster

That's what I thought, but this is what I got:

    > # differentially expressed genes list



   > degs <- as.vector(subset(drst, FDR < 0.25)[[1]])

    > # do GO analysis
    > go <- goana(degs, species="Hs");

    > tgo <- topGO(go);

    > # do KEGG analysis
    > keg <- kegga(degs, species="Hs");
    Error in eval(expr, envir, enclos) : could not find function "kegga"

So it looks like kegga is not installed.

Thanks.

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written by dr.genetics dr.genetics

Dear @WouterDeCoster, maybe it depends to the version of R or Bioconductor or edgeR is not installed at all?

Is there any command to check which packages are already installed via limma or edgeR in a system ?

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written by Farbod Farbod

It's probably a version thing, see my other comment. I think sessionInfo() is the command you are looking for to see what is already loaded. But kegga is not a package, it's a function. So it will not show up in sessionInfo(). (The command works for me with only edgeR explicitly loaded.)

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written by WouterDeCoster WouterDeCoster

it works for me too.

Now that we have the kegga.r script (I have provided it above), can we introduce it manually in our script when running edgeR?

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written by Farbod Farbod

Theoretically yes, but then we need to make sure that all dependencies are also properly installed. Let's first see if @dr.genetics has the latest versions of R, bioconductor and edgeR. That will likely explain the problem, and if not we can try a manual way as you suggest.

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written by WouterDeCoster WouterDeCoster

You should have a look which R version and which version of edgeR you have loaded. Do this by running sessionInfo() in an R terminal. If it isn't the latest version of edgeR (3.14.0), update the package and see if that helps. Update, just like installing, by

source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")

Also, if you R version is very outdated, it's usually a good idea to have that updated.

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written by WouterDeCoster WouterDeCoster

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