5.1 years ago by
Looking at the vignette for OmicCircos, there is an example mapping file on page 4, and the vignette states that the second column ('Po' column) is the position. It's not clear what 'position' means in this context, so let's do an experiment!
The first gene is ISG15. I don't see the build, but it is TCGA data, so I assume it is a bit old, probably hg18. So I went to UCSC's browser, punched in that gene name and got:
ISG15 (uc001acj.2) at chr1:938710-939782
as the first hit for the hg18 build. But the value in the vignette is 939245.5, which is somewhere between the start and end of that gene. So I used my trusty slide rule to calculate the mean of the start/end value that I get from UCSC, and I get 939246, which is close enough for government work. So I assume that the position is the middle of the gene, which you can easily compute if you have the start/end values.