Question: M3D package in Bioconductor 3.4
0
gravatar for francescacairoli
2.9 years ago by
francescacairoli0 wrote:

Hello,

I'm trying to use the 'M3D' package. I've tried with the Bioconductor 3.2 release and everything works fine as in the M3D tutorial.

But when I tried with the release 3.4 I get the following message:

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

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("M3D")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21).

Installing package(s) ‘M3D’

Package which is only available in source form, and may need

  compilation of C/C++/Fortran: ‘M3D’

  These will not be installed.

 

I need to use the function 'readBedFiles' which is in the new version only. Do you have any idea on what's the problem and on how I can solve it?

Thank you very much for your time.

 

 

 

methylation bioconductor • 624 views
ADD COMMENTlink modified 2.9 years ago by Dimitris Polychronopoulos50 • written 2.9 years ago by francescacairoli0
Answer: M3D package in Bioconductor 3.4
1
gravatar for Steve Lianoglou
2.9 years ago by
Denali
Steve Lianoglou12k wrote:

The rtracklayer package provides rather versatile methods to import a large number of file types used in genomics, bed files certainly being one of them.

If all you need is to import BED files, than try the import (or direct call to import.bed) function it provides to do that.

ADD COMMENTlink written 2.9 years ago by Steve Lianoglou12k
Answer: M3D package in Bioconductor 3.4
0
gravatar for francescacairoli
2.9 years ago by
francescacairoli0 wrote:
No, I need to use the M3D package, but I cannot use the older versione because my bed files are not in the Encode format, so I need to use the newly created function to read bed bed files with format differenti from Encode, which is in the 3.4 release.
ADD COMMENTlink written 2.9 years ago by francescacairoli0

If you want to comment on a post, please use the ADD COMMENT button, rather than the 'Add your answer' box below, which is for answers.

I assume you are on Windows, as M3D is failing check on that OS. Since you didn't use the M3D tag for your question, it's possible that Tom Mayo, the maintainer for the package didn't see your question. You might consider emailing him directly and asking him to fix his package so it passes check on Windows. You can get his email at the M3D landing page.

ADD REPLYlink written 2.9 years ago by James W. MacDonald51k
Answer: M3D package in Bioconductor 3.4
0
gravatar for Dimitris Polychronopoulos
2.9 years ago by
United Kingdom

You could also try the following to see if they work for you:

genomation::readBed

genomation::readBroadPeak

genomation::readNarrowPeak

LOLA::readBed

CNEr::readBed

 

 

ADD COMMENTlink written 2.9 years ago by Dimitris Polychronopoulos50
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