Entering edit mode
Dear Tatiana,
You can use BED2RangedData to convert the BED format for
annotatePeakInBatch.
FYI, here is a list of FAQ about ChIPpeakAnno
http://pgfe.umassmed.edu/ChIPpeakAnno/FAQ.html
Best regards,
Julie
On 5/28/13 8:51 AM, "Subkhankulova, Tatiana"
<t.subkhankulova@imperial.ac.uk> wrote:
Dear Julie,
I have read your ChIPpeakAnno users guide. It seems very helpful in
annotation ChIP-seq peaks. However, I had a problem in generation of
input data for the R-analysis. Would it be possible for you to let me
know how did you make the object myPeakList? Did you use initially
BED, TXT of any other format? Currently, I can get BAM, BED, WIG or
TXT files, which contain information about ChIP peaks, though I do
not know how transform any of them to R-input object.
Please help,
Many thanks in advance,
Dr T Subkhankulova
Heart Science
National Heart and Lung Institute
Imperial College
Imperial Centre for Translational and Experimental Medicine,
3rd Floor
Office 322, Lab 304
Hammersmith Hospital Campus
Du Cane Road
London W12 0NN
Tel: +44(0)2075941825
E-mail: tsubkhan@imperial.ac.uk <mailto:tsubkhan@imperial.ac.uk>
Mob: 07758370590
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