Question: How to install kegga for edgeR?
0
gravatar for dr.genetics
3.1 years ago by
dr.genetics60
dr.genetics60 wrote:

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!

gene rna-seq R software error • 1.2k views
ADD COMMENTlink modified 3.1 years ago by WouterDeCoster42k • written 3.1 years ago by dr.genetics60

Hi Dr.genetics

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

ADD REPLYlink written 3.1 years ago by Farbod3.3k

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

ADD REPLYlink written 3.1 years ago by dr.genetics60

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Farbod3.3k
1
gravatar for WouterDeCoster
3.1 years ago by
Belgium
WouterDeCoster42k wrote:

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.

ADD COMMENTlink written 3.1 years ago by WouterDeCoster42k

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.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by dr.genetics60
1

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Also, if you R version is very outdated, it's usually a good idea to have that updated.

ADD REPLYlink written 3.1 years ago by WouterDeCoster42k

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 ?

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Farbod3.3k
1

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.)

ADD REPLYlink written 3.1 years ago by WouterDeCoster42k

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?

ADD REPLYlink written 3.1 years ago by Farbod3.3k

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.

ADD REPLYlink written 3.1 years ago by WouterDeCoster42k
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