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Question: Run windowCounts only on annotated regions?
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gravatar for endrebak85
15 months ago by
endrebak8530
endrebak8530 wrote:

I want to run windowCounts only on some annotated regions. Is this possible?

readParams has a discard-option, but not one for include...

Thanks. 

ADD COMMENTlink modified 15 months ago by Aaron Lun19k • written 15 months ago by endrebak8530
2
gravatar for Aaron Lun
15 months ago by
Aaron Lun19k
Cambridge, United Kingdom
Aaron Lun19k wrote:

No. The closest you can get is to run windowCounts on the whole genome (or selected chromosomes), and then to apply findOverlaps to select windows that overlap your regions of interest. Depending on what you want to use the counts for, it may be more appropriate to construct bin/window intervals yourself and to apply regionCounts, e.g., as described in A: Use csaw to build matrix for heatmap?.

ADD COMMENTlink written 15 months ago by Aaron Lun19k

Thanks, csaw is wonderful.

ADD REPLYlink written 15 months ago by endrebak8530
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