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.

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,