New to R: How to use your own data for Bioconductor Packages
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hseepany • 0
@hseepany-8704
Last seen 5.0 years ago

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.

MEDIPS rsamtools • 763 views
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Hi hseepany,

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

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@guillaume-devailly-8722
Last seen 11 days ago
Toulouse, France

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,