does import.bw with the selection argument take into account strand?
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maltethodberg ▴ 140
@maltethodberg-9690
Last seen 1 day ago
Denmark

I'm generating mean coverage plots for promoters based on some BigWig files, like so:

import(con=bwFile, selection=BigWigSelection(promoters), as="NumericList) %>% do.call(rbind,.)

Which gives me a matrix of the coverage for each promoter at each position. Does the import.bw function reverse the signal of the promoters on the minus strand, or do I need to do this myself?

 

 

 

 

 

rtracklayer import.bw • 498 views
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@michael-lawrence-3846
Last seen 12 weeks ago
United States

You need to do it yourself.

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I should add that it's pretty easy to do this with revElements() on the returned list. The main issue is that BigWigSelection only indicates a list of ranges; the strand information from the GRanges is discarded during construction. At least right now, this behavior is consistent with GRanges-based extraction from Lists, e.g. RleList, NumericList, etc. It is worth revisiting though.

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