Question: Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
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gravatar for 835102330
2.2 years ago by
8351023300
8351023300 wrote:

Soggi  regionPlot function gave error when import bigwig file  with "percentOfRegion" mode, my codes is as followings,

hipExample <- regionPlot("out.bw",testRanges = genes_gr,format = "bigwig",distanceUp = 0,distanceDown = 0,style = "percentOfRegion")

Importing BigWig.....Done
Filtering regions which extend outside of genome boundaries.....Done
Filtered 7515 of 33323 regions
Splitting regions by Watson and Crick strand....Done
..Done
Found 12982 Watson strand regions
Found 12826 Crick strand regions
Extending regions.....done
Making windows.
Windowing positive 5' flanking 
Windowing positive regions 
Windowing positive 3' flank 
Windowing negative 5' flank 
Windowing negative regions 
Windowing negative 3' flank 
..done

Calculating bin scores for regions.
Processing per contig
contig: 1
Processing inner region windows in Chr1
..done
Processing flanking windows in Chr1
contig: 2
Processing inner region windows in Chr2
..done
Processing flanking windows in Chr2
contig: 3
Processing inner region windows in Chr3
..done
Processing flanking windows in Chr3
contig: 4
Processing inner region windows in Chr4
..done
Processing flanking windows in Chr4
Error in FUN(X[[i]], ...) : 
  assay rownames() must be NULL or equal rowData rownames() / rowRanges names()

 

 

chip-seq region soggi • 654 views
ADD COMMENTlink modified 2.2 years ago by Thomas Carroll400 • written 2.2 years ago by 8351023300
Answer: Soggi regionPlot function gave error when import bigwig file with "percentOfRe
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gravatar for Thomas Carroll
2.2 years ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:

hi,

I will try and recreate this problem with some local data and get back to you tomorrow.

best,

tom

ADD COMMENTlink written 2.2 years ago by Thomas Carroll400
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