Problems With Bioconductor'S Genomicfeatures Package
3
0
Entering edit mode
10.1 years ago
Travis ★ 2.8k

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.

r bioconductor next-gen sequencing rna • 4.8k views
ADD COMMENT
3
Entering edit mode
10.1 years ago
Ido Tamir 5.2k

But you did load the library with?:

library("GenomicFeatures")

you can check for installed packages with:

installed.packages()
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

@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)

ADD REPLY
0
Entering edit mode
10.1 years ago
Neilfws 49k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

library(help="GenomicFeatures")

ADD REPLY
0
Entering edit mode
5.0 years ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 1665 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6