Problems With Bioconductor'S Genomicfeatures Package

Question

[Travis]

Hi all,

I am very new to R/Bioconductor but am currently attempting some RNA-Seq analysis with it for the sake of education.

Unfortunately I am having issues getting the GenomicFeatures package to work.

I have installed it using

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")

and the install seems to work ok but when I try using any of the methods e.g. 'makeTranscriptDbFromUCSC'I just get an error message like

Error: could not find function "makeTranscriptDbFromUCSC"

Can anyone help in diagnosing or correcting the problem?

Thanks in advance.

Answer 1

[Ido Tamir]

But you did load the library with?:

library("GenomicFeatures")

you can check for installed packages with:

installed.packages()

[Travis]

Hi. Yes, I have loaded the library and installed.packages() shows it as installed but the problem exists nonetheless!

[Ido Tamir]

But then, check if its a recent version (I don't know when this function was added). biocLite always matches R versions with bioconductor versions. Maybe you have an old R.

[Travis]

R is version 2.9.2 so pretty old I guess? I can just imagine the fun I'm going to have getting the IS guys to update this on our server.

[Istvan Albert]

@Travis: You can always install your own version of R.

[Travis]

How is that? I don't have sufficient privileges on the server & even my desktop lacks a number of dependencies which I can't currently correct because of our internal setup. The joys of industry.

[Steve Lianoglou]

@Travis: You can compile it into your home directory. I typically create an sw directory that I use as a prefix for custom installs, as you grow your "home library", you'll get the ~/sw/etc ~/sw/bin, etc. in there, and you juust add ~/sw/bin to your PATH. For instance, to install R locally, just d/l the latest sources and simply do a configure --prefix=/home/YOU/sw; make; make install (more or less)

Answer 2

[Neilfws]

I cannot reproduce this using R 2.13 and Bioconductor 2.8.

The error message strongly suggests that the library is not loaded. I can only reproduce it if I do not run:

library("GenomicFeatures")

As suggested by Ido.

[Travis]

As I mentioned above, it might indeed be my R version. I definitely have run the library("GenomicFeatures") command though :)

[Neilfws]

If you're sure that the library has loaded, try typing "GenomicFeatures" then hitting the tab key a couple of times; that should display the available functions.

[Travis]

I can type "Ge" and tab will automatically complete "GenomicFeatures::" for me but after that it does nothing - no functions appear!

[Travis]

I can type "Ge" and tab will automatically complete "GenomicFeatures::" for me but after that tab does nothing - no functions will appear!

[Ido Tamir]

library(help="GenomicFeatures")

Answer 3

[Stephane Plaisance]

The function is indeed in GenomicFeatures but has been slightly renamed to 'makeTxDbFromUCSC'