Data analysis in R
1
0
Entering edit mode
@efraimculfa-12081
Last seen 7.9 years ago

I want to analyse my RSQ lite data (generated in Galaxy)  in R. But I keep getting this error. Could someone pelase help me sort this out?

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

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘cummeRbund’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/cummeRbund_2.16.0.zip'
Content type 'application/zip' length 7436796 bytes (7.1 MB)
downloaded 7.1 MB

package ‘cummeRbund’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Efraim Culfa\AppData\Local\Temp\RtmpucYSiN\downloaded_packages
> cuff_data<-readCufflinks('D:\\AAA-PengZhou\\R-3.0.1\\library\\AAAAAA')
Error: could not find function "readCufflinks"

bioconductor next-generation sequencing galaxy • 1.5k views
ADD COMMENT
0
Entering edit mode

Please load cummeRbund after you installed it: 

 

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

biocLite("cummeRbund")

library(cummeRbund)

cuff_data<-readCufflinks('D:\\AAA-PengZhou\\R-3.0.1\\library\\AAAAAA')

 

If you are still having trouble, Please also include your sessionInfo() 

ADD REPLY
0
Entering edit mode
@schifferl
Last seen 7 months ago
New York, NY

You have a number of issues, but importantly you are installing Bioconductor at the top of your script, which is unnecessary. But if you don't have Bioconductor installed, do it like this:

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

I aways restart R after this with Ctl-Shift-0 or Cmd-Shift-0, if using RStudio.

Then you can install and use cummeRbund like so:

BiocInstaller::biocLite("cummeRbund")
cummeRbund::readCufflinks("whateverFileYouWant")

Or this syntax will do the same:

library(BiocInstaller)
biocLite("cummeRbund")
library(cummeRbund)
readCufflinks("whateverFileYouWant")
ADD COMMENT

Login before adding your answer.

Traffic: 639 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