Question: New to R: How to use your own data for Bioconductor Packages
0
gravatar for hseepany
4.3 years ago by
hseepany0
Canada
hseepany0 wrote:

Hi,

I am new to R and programming and I have a couple of BAM files that I wanted to use to look at methylation patterns using MEDIPS. I was wondering how can I use my BAM files to compare the data. When I add my file location to the commands, it does not work. Please help. It will also be very helpful if you can give me as much detail as possible, as I am very new to this.

Thank you and I appreciate your help.

 

rsamtools medips • 602 views
ADD COMMENTlink modified 4.3 years ago by Dan Tenenbaum8.2k • written 4.3 years ago by hseepany0

Hi hseepany,

can you please specify what exactly you want to do, what commands you tried to apply, and the error message you received.

ADD REPLYlink written 4.3 years ago by Matthias Lienhard140
Answer: New to R: How to use your own data for Bioconductor Packages
0
gravatar for Guillaume Devailly
4.3 years ago by
United Kingdom
Guillaume Devailly0 wrote:

Many possible solutions.

For example, using Repitools (http://www.bioconductor.org/packages/release/bioc/html/Repitools.html):

paths <- c("MeDP.bam", "control.bam")

myDataInR <- BAM2GrangesList(paths)

I also recommend Repitools documentation, including the old Rforge one (even if a few function where renamed since):

http://repitools.r-forge.r-project.org/RepitoolsManual.pdf

Cheers,

ADD COMMENTlink written 4.3 years ago by Guillaume Devailly0
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