How to install kegga for edgeR?

Question

[dr.genetics]

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!

[Farbod]

Hi Dr.genetics

Are you searching for kegga R package or How to use it in DEG and pathway analysis ?

[dr.genetics]

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

[Farbod]

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

Answer 1

[WouterDeCoster]

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.

[dr.genetics]

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.

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Also, if you R version is very outdated, it's usually a good idea to have that updated.

[Farbod]

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 ?

[WouterDeCoster]

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.)

[Farbod]

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?

[WouterDeCoster]

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.