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Hi,
I would like to visualize not the GC content but CpG content in a track of Gviz, for example.
Do you have an idea to do that ?
Regards,
Tiphaine
Hi,
I would like to visualize not the GC content but CpG content in a track of Gviz, for example.
Do you have an idea to do that ?
Regards,
Tiphaine
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I'm not sure if this is exactly what you want, but this function takes a BSgenome instance, a chromosome, and a tile width, and calculated CpG % in windows across a particular chromosome
This would seem to be a relatively effective way to quickly visualize CpG content, e.g.,
Another formulation might slide rather than tile the window across coverage, along the lines of
I'm not sure how to visualize this with Gviz; for smaller regions one might use
getSeq()
to get the DNA sequence of the specific region.