Question: How to plot an ideogram for two bed files with different number of rows in R?
gravatar for mohamad.merhi96
20 months ago by
mohamad.merhi960 wrote:

I'm trying to create an ideogram for human vs mouse to recognise the common and different transcription factor binding sites . I have two bed files representing starts and ends of transcription factor binding sites. My problem is that the human bed file is larger than the mouse one.

I need them to have the same number of rows otherwise RCircos will produce an error saying that the number of rows in the two datasets are different.. "arguments imply differing number of rows"

Any suggestions?

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ADD COMMENTlink modified 20 months ago by Alex Reynolds28k • written 20 months ago by mohamad.merhi960
gravatar for Alex Reynolds
20 months ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

Cutting out rows in one subset doesn't really make sense. You need different ideograms for the two species, and show the alignment of chromosomes between species, where there are deletions, insertions, and novel regions unique to the species. You could use UCSC's ideogram graphing tool, or write one with Circos, say, to display chain tracks that display the alignment of genomic intervals for two species (human and mouse). Then plot your species-specific TF binding sites atop each per-species ideogram.

ADD COMMENTlink written 20 months ago by Alex Reynolds28k

Frankly I don't think approaching the problem using Circos that way is feasible ? I'm not quite sure, I used leftover chains to produce my mouse bed file from my human bed file , wouldn't it be backtracking to use the leftover chains? Additionally I didn't quite get the visual product of the Circos suggestion.

ADD REPLYlink modified 20 months ago • written 20 months ago by mohamad.merhi960
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