Question: Cleaning up DiffBind counts in relation to chromosome map
0
gravatar for rbronste
24 months ago by
rbronste60
rbronste60 wrote:

Wondering how I can go about outputting the following command which would have the chromosome map already applied? So for instance instead of "chromosome # 26" representing the X, it is already changed in the binding matrix following counting, or is this only possible in post-processing (e.g. editing the csv output)? Thanks!

ChIP_count$binding

 

 

ADD COMMENTlink modified 24 months ago by Rory Stark2.9k • written 24 months ago by rbronste60
Answer: Cleaning up DiffBind counts in relation to chromosome map
2
gravatar for Rory Stark
24 months ago by
Rory Stark2.9k
CRUK, Cambridge, UK
Rory Stark2.9k wrote:

You can use dba.peakset() with bRetrieve=TRUE. This will return the binding matrix with the chromosome names in it. By default this is returned as a GRanges object; if you set DataType=DBA_DATA_FRAME it will return a dataframe.

ADD COMMENTlink written 24 months ago by Rory Stark2.9k

Thanks, exactly what I needed!

ADD REPLYlink written 24 months ago by rbronste60
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