Question

Run windowCounts only on annotated regions?

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endrebak85 ▴ 40

@endrebak85-10660

Last seen 5.2 years ago

github.com/endrebak/

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

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

Thanks.

csaw • 1.1k views

ADD COMMENT • link updated 7.7 years ago by Aaron Lun ★ 28k • written 7.7 years ago by endrebak85 ▴ 40

score 2 · Accepted Answer · 2017-02-21

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Aaron Lun ★ 28k

@alun

Last seen 16 hours ago

The city by the bay

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?.